{ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://catalog.lintel.tools/schemas/schemastore/bioimageio-resource-description/latest.json", "x-lintel": { "source": "https://bioimage-io.github.io/spec-bioimage-io/bioimageio_schema_latest.json", "sourceSha256": "5e6d1810f498b38686e0bc72cdc88c77f21272c240a343ffc8513670270639b3", "fileMatch": [ "bioimageio.yaml", "*.bioimageio.yaml" ], "parsers": [ "yaml" ] }, "$defs": { "ArchitectureFromFileDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "Architecture source file", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "callable": { "description": "Identifier of the callable that returns a torch.nn.Module instance.", "examples": [ "MyNetworkClass", "get_my_model" ], "minLength": 1, "title": "Identifier", "type": "string" }, "kwargs": { "type": "object", "description": "key word arguments for the `callable`", "title": "Kwargs", "additionalProperties": { "$ref": "#/$defs/YamlValue" } } }, "required": [ "source", "callable" ], "title": "model.v0_5.ArchitectureFromFileDescr", "additionalProperties": false }, "ArchitectureFromLibraryDescr": { "type": "object", "properties": { "callable": { "description": "Identifier of the callable that returns a torch.nn.Module instance.", "examples": [ "MyNetworkClass", "get_my_model" ], "minLength": 1, "title": "Identifier", "type": "string" }, "kwargs": { "type": "object", "description": "key word arguments for the `callable`", "title": "Kwargs", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "import_from": { "description": "Where to import the callable from, i.e. `from import `", "title": "Import From", "type": "string" } }, "required": [ "callable", "import_from" ], "title": "model.v0_5.ArchitectureFromLibraryDescr", "additionalProperties": false }, "AttachmentsDescr": { "type": "object", "properties": { "files": { "description": "File attachments", "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Files", "type": "array" } }, "title": "generic.v0_2.AttachmentsDescr", "additionalProperties": true }, "BadgeDescr": { "type": "object", "description": "A custom badge", "properties": { "label": { "description": "badge label to display on hover", "examples": [ "Open in Colab" ], "title": "Label", "type": "string" }, "icon": { "anyOf": [ { "format": "file-path", "title": "FilePath", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "format": "uri", "maxLength": 2083, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "badge icon (included in bioimage.io package if not a URL)", "examples": [ "https://colab.research.google.com/assets/colab-badge.svg" ], "title": "Icon" }, "url": { "description": "target URL", "examples": [ "https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb" ], "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" } }, "required": [ "label", "url" ], "title": "generic.v0_2.BadgeDescr", "additionalProperties": false }, "BatchAxis": { "type": "object", "properties": { "id": { "default": "batch", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "batch", "title": "Type", "type": "string" }, "size": { "anyOf": [ { "const": 1, "type": "integer" }, { "type": "null" } ], "default": null, "description": "The batch size may be fixed to 1,\notherwise (the default) it may be chosen arbitrarily depending on available memory", "title": "Size" } }, "required": [ "type" ], "title": "model.v0_5.BatchAxis", "additionalProperties": false }, "BiasRisksLimitations": { "type": "object", "description": "Known biases, risks, technical limitations, and recommendations for model use.", "properties": { "known_biases": { "default": "In general bioimage models may suffer from biases caused by:\n\n- Imaging protocol dependencies\n- Use of a specific cell type\n- Species-specific training data limitations\n\n", "description": "Biases in training data or model behavior.", "title": "Known Biases", "type": "string" }, "risks": { "default": "Common risks in bioimage analysis include:\n\n- Erroneously assuming generalization to unseen experimental conditions\n- Trusting (overconfident) model outputs without validation\n- Misinterpretation of results\n\n", "description": "Potential risks in the context of bioimage analysis.", "title": "Risks", "type": "string" }, "limitations": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Technical limitations and failure modes.", "title": "Limitations" }, "recommendations": { "default": "Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model.", "description": "Mitigation strategies regarding `known_biases`, `risks`, and `limitations`, as well as applicable best practices.\n\nConsider:\n- How to use a validation dataset?\n- How to manually validate?\n- Feasibility of domain adaptation for different experimental setups?", "title": "Recommendations", "type": "string" } }, "title": "model.v0_5.BiasRisksLimitations", "additionalProperties": true }, "BinarizeAlongAxisKwargs": { "type": "object", "description": "key word arguments for `BinarizeDescr`", "properties": { "threshold": { "description": "The fixed threshold values along `axis`", "items": { "type": "number" }, "minItems": 1, "title": "Threshold", "type": "array" }, "axis": { "description": "The `threshold` axis", "examples": [ "channel" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" } }, "required": [ "threshold", "axis" ], "title": "model.v0_5.BinarizeAlongAxisKwargs", "additionalProperties": false }, "ChannelAxis": { "type": "object", "properties": { "id": { "default": "channel", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "channel", "title": "Type", "type": "string" }, "channel_names": { "items": { "minLength": 1, "title": "Identifier", "type": "string" }, "minItems": 1, "title": "Channel Names", "type": "array" } }, "required": [ "type", "channel_names" ], "title": "model.v0_5.ChannelAxis", "additionalProperties": false }, "DataDependentSize": { "type": "object", "properties": { "min": { "default": 1, "exclusiveMinimum": 0, "title": "Min", "type": "integer" }, "max": { "anyOf": [ { "exclusiveMinimum": 1, "type": "integer" }, { "type": "null" } ], "default": null, "title": "Max" } }, "title": "model.v0_5.DataDependentSize", "additionalProperties": false }, "Datetime": { "description": "Timestamp in [ISO 8601](# format\nwith a few restrictions listed [here](https://docs.python.org/3/library/datetime.html#datetime.datetime.fromisoformat).", "format": "date-time", "title": "Datetime", "type": "string" }, "EnsureDtypeDescr": { "type": "object", "description": "Cast the tensor data type to `EnsureDtypeKwargs.dtype` (if not matching).\n\nThis can for example be used to ensure the inner neural network model gets a\ndifferent input tensor data type than the fully described bioimage.io model does.\n\nExamples:\n The described bioimage.io model (incl. preprocessing) accepts any\n float32-compatible tensor, normalizes it with percentiles and clipping and then\n casts it to uint8, which is what the neural network in this example expects.\n - in YAML\n ```yaml\n inputs:\n - data:\n type: float32 # described bioimage.io model is compatible with any float32 input tensor\n preprocessing:\n - id: scale_range\n kwargs:\n axes: ['y', 'x']\n max_percentile: 99.8\n min_percentile: 5.0\n - id: clip\n kwargs:\n min: 0.0\n max: 1.0\n - id: ensure_dtype # the neural network of the model requires uint8\n kwargs:\n dtype: uint8\n ```\n - in Python:\n >>> preprocessing = [\n ... ScaleRangeDescr(\n ... kwargs=ScaleRangeKwargs(\n ... axes= (AxisId('y'), AxisId('x')),\n ... max_percentile= 99.8,\n ... min_percentile= 5.0,\n ... )\n ... ),\n ... ClipDescr(kwargs=ClipKwargs(min=0.0, max=1.0)),\n ... EnsureDtypeDescr(kwargs=EnsureDtypeKwargs(dtype=\"uint8\")),\n ... ]", "properties": { "id": { "const": "ensure_dtype", "title": "Id", "type": "string" }, "kwargs": { "$ref": "#/$defs/EnsureDtypeKwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.EnsureDtypeDescr", "additionalProperties": false }, "EnsureDtypeKwargs": { "type": "object", "description": "key word arguments for `EnsureDtypeDescr`", "properties": { "dtype": { "enum": [ "float32", "float64", "uint8", "int8", "uint16", "int16", "uint32", "int32", "uint64", "int64", "bool" ], "title": "Dtype", "type": "string" } }, "required": [ "dtype" ], "title": "model.v0_5.EnsureDtypeKwargs", "additionalProperties": false }, "EnvironmentalImpact": { "type": "object", "description": "Environmental considerations for model training and deployment.\n\nCarbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).", "properties": { "hardware_type": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "GPU/CPU specifications", "title": "Hardware Type" }, "hours_used": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Total compute hours", "title": "Hours Used" }, "cloud_provider": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "If applicable", "title": "Cloud Provider" }, "compute_region": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Geographic location", "title": "Compute Region" }, "co2_emitted": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "kg CO2 equivalent\n\nCarbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).", "title": "Co2 Emitted" } }, "title": "model.v0_5.EnvironmentalImpact", "additionalProperties": true }, "Evaluation": { "type": "object", "properties": { "model_id": { "anyOf": [ { "minLength": 1, "title": "ModelId", "type": "string" }, { "type": "null" } ], "default": null, "description": "Model being evaluated.", "title": "Model Id" }, "dataset_id": { "description": "Dataset used for evaluation.", "minLength": 1, "title": "DatasetId", "type": "string" }, "dataset_source": { "description": "Source of the dataset.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, "dataset_role": { "description": "Role of the dataset used for evaluation.\n\n- `train`: dataset was (part of) the training data\n- `validation`: dataset was (part of) the validation data used during training, e.g. used for model selection or hyperparameter tuning\n- `test`: dataset was (part of) the designated test data; not used during training or validation, but acquired from the same source/distribution as training data\n- `independent`: dataset is entirely independent test data; not used during training or validation, and acquired from a different source/distribution than training data\n- `unknown`: role of the dataset is unknown; choose this if you are not certain if (a subset) of the data was seen by the model during training.", "enum": [ "train", "validation", "test", "independent", "unknown" ], "title": "Dataset Role", "type": "string" }, "sample_count": { "description": "Number of evaluated samples.", "title": "Sample Count", "type": "integer" }, "evaluation_factors": { "description": "(Abbreviations of) each evaluation factor.\n\nEvaluation factors are criteria along which model performance is evaluated, e.g. different image conditions\nlike 'low SNR', 'high cell density', or different biological conditions like 'cell type A', 'cell type B'.\nAn 'overall' factor may be included to summarize performance across all conditions.", "items": { "maxLength": 16, "type": "string" }, "title": "Evaluation Factors", "type": "array" }, "evaluation_factors_long": { "description": "Descriptions (long form) of each evaluation factor.", "items": { "type": "string" }, "title": "Evaluation Factors Long", "type": "array" }, "metrics": { "description": "(Abbreviations of) metrics used for evaluation.", "items": { "maxLength": 16, "type": "string" }, "title": "Metrics", "type": "array" }, "metrics_long": { "description": "Description of each metric used.", "items": { "type": "string" }, "title": "Metrics Long", "type": "array" }, "results": { "description": "Results for each metric (rows; outer list) and each evaluation factor (columns; inner list).", "items": { "items": { "anyOf": [ { "type": "string" }, { "type": "number" }, { "type": "integer" } ] }, "type": "array" }, "title": "Results", "type": "array" }, "results_summary": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Interpretation of results for general audience.\n\nConsider:\n - Overall model performance\n - Comparison to existing methods\n - Limitations and areas for improvement", "title": "Results Summary" } }, "required": [ "dataset_id", "dataset_source", "dataset_role", "sample_count", "evaluation_factors", "evaluation_factors_long", "metrics", "metrics_long", "results" ], "title": "model.v0_5.Evaluation", "additionalProperties": true }, "FileDescr": { "type": "object", "description": "A file description", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "File source", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" } }, "required": [ "source" ], "title": "_internal.io.FileDescr", "additionalProperties": false }, "FixedZeroMeanUnitVarianceAlongAxisKwargs": { "type": "object", "description": "key word arguments for `FixedZeroMeanUnitVarianceDescr`", "properties": { "mean": { "description": "The mean value(s) to normalize with.", "items": { "type": "number" }, "minItems": 1, "title": "Mean", "type": "array" }, "std": { "description": "The standard deviation value(s) to normalize with.\nSize must match `mean` values.", "items": { "minimum": 1e-6, "type": "number" }, "minItems": 1, "title": "Std", "type": "array" }, "axis": { "description": "The axis of the mean/std values to normalize each entry along that dimension\nseparately.", "examples": [ "channel", "index" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" } }, "required": [ "mean", "std", "axis" ], "title": "model.v0_5.FixedZeroMeanUnitVarianceAlongAxisKwargs", "additionalProperties": false }, "FixedZeroMeanUnitVarianceDescr": { "type": "object", "description": "Subtract a given mean and divide by the standard deviation.\n\nNormalize with fixed, precomputed values for\n`FixedZeroMeanUnitVarianceKwargs.mean` and `FixedZeroMeanUnitVarianceKwargs.std`\nUse `FixedZeroMeanUnitVarianceAlongAxisKwargs` for independent scaling along given\naxes.\n\nExamples:\n1. scalar value for whole tensor\n - in YAML\n ```yaml\n preprocessing:\n - id: fixed_zero_mean_unit_variance\n kwargs:\n mean: 103.5\n std: 13.7\n ```\n - in Python\n >>> preprocessing = [FixedZeroMeanUnitVarianceDescr(\n ... kwargs=FixedZeroMeanUnitVarianceKwargs(mean=103.5, std=13.7)\n ... )]\n\n2. independently along an axis\n - in YAML\n ```yaml\n preprocessing:\n - id: fixed_zero_mean_unit_variance\n kwargs:\n axis: channel\n mean: [101.5, 102.5, 103.5]\n std: [11.7, 12.7, 13.7]\n ```\n - in Python\n >>> preprocessing = [FixedZeroMeanUnitVarianceDescr(\n ... kwargs=FixedZeroMeanUnitVarianceAlongAxisKwargs(\n ... axis=AxisId(\"channel\"),\n ... mean=[101.5, 102.5, 103.5],\n ... std=[11.7, 12.7, 13.7],\n ... )\n ... )]", "properties": { "id": { "const": "fixed_zero_mean_unit_variance", "title": "Id", "type": "string" }, "kwargs": { "anyOf": [ { "$ref": "#/$defs/FixedZeroMeanUnitVarianceKwargs" }, { "$ref": "#/$defs/FixedZeroMeanUnitVarianceAlongAxisKwargs" } ], "title": "Kwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.FixedZeroMeanUnitVarianceDescr", "additionalProperties": false }, "FixedZeroMeanUnitVarianceKwargs": { "type": "object", "description": "key word arguments for `FixedZeroMeanUnitVarianceDescr`", "properties": { "mean": { "description": "The mean value to normalize with.", "title": "Mean", "type": "number" }, "std": { "description": "The standard deviation value to normalize with.", "minimum": 1e-6, "title": "Std", "type": "number" } }, "required": [ "mean", "std" ], "title": "model.v0_5.FixedZeroMeanUnitVarianceKwargs", "additionalProperties": false }, "ImplicitOutputShape": { "type": "object", "description": "Output tensor shape depending on an input tensor shape.\n`shape(output_tensor) = shape(input_tensor) * scale + 2 * offset`", "properties": { "reference_tensor": { "description": "Name of the reference tensor.", "minLength": 1, "title": "TensorName", "type": "string" }, "scale": { "description": "output_pix/input_pix for each dimension.\n'null' values indicate new dimensions, whose length is defined by 2*`offset`", "items": { "anyOf": [ { "type": "number" }, { "type": "null" } ] }, "minItems": 1, "title": "Scale", "type": "array" }, "offset": { "description": "Position of origin wrt to input.", "items": { "anyOf": [ { "type": "integer" }, { "multipleOf": 0.5, "type": "number" } ] }, "minItems": 1, "title": "Offset", "type": "array" } }, "required": [ "reference_tensor", "scale", "offset" ], "title": "model.v0_4.ImplicitOutputShape", "additionalProperties": false }, "IndexInputAxis": { "type": "object", "properties": { "size": { "anyOf": [ { "exclusiveMinimum": 0, "type": "integer" }, { "$ref": "#/$defs/ParameterizedSize" }, { "$ref": "#/$defs/SizeReference" } ], "description": "The size/length of this axis can be specified as\n- fixed integer\n- parameterized series of valid sizes (`ParameterizedSize`)\n- reference to another axis with an optional offset (`SizeReference`)", "examples": [ 10, { "min": 32, "step": 16 }, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ], "title": "Size" }, "id": { "default": "index", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "index", "title": "Type", "type": "string" }, "concatenable": { "default": false, "description": "If a model has a `concatenable` input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a `SizeReference` to a concatenable\ninput axis.", "title": "Concatenable", "type": "boolean" } }, "required": [ "size", "type" ], "title": "model.v0_5.IndexInputAxis", "additionalProperties": false }, "IndexOutputAxis": { "type": "object", "properties": { "id": { "default": "index", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "index", "title": "Type", "type": "string" }, "size": { "anyOf": [ { "exclusiveMinimum": 0, "type": "integer" }, { "$ref": "#/$defs/SizeReference" }, { "$ref": "#/$defs/DataDependentSize" } ], "description": "The size/length of this axis can be specified as\n- fixed integer\n- reference to another axis with an optional offset (`SizeReference`)\n- data dependent size using `DataDependentSize` (size is only known after model inference)", "examples": [ 10, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ], "title": "Size" } }, "required": [ "type", "size" ], "title": "model.v0_5.IndexOutputAxis", "additionalProperties": false }, "IntervalOrRatioDataDescr": { "type": "object", "properties": { "type": { "default": "float32", "enum": [ "float32", "float64", "uint8", "int8", "uint16", "int16", "uint32", "int32", "uint64", "int64" ], "examples": [ "float32", "float64", "uint8", "uint16" ], "title": "Type", "type": "string" }, "range": { "default": [ null, null ], "description": "Tuple `(minimum, maximum)` specifying the allowed range of the data in this tensor.\n`None` corresponds to min/max of what can be expressed by **type**.", "maxItems": 2, "minItems": 2, "prefixItems": [ { "anyOf": [ { "type": "number" }, { "type": "null" } ] }, { "anyOf": [ { "type": "number" }, { "type": "null" } ] } ], "title": "Range", "type": "array" }, "unit": { "anyOf": [ { "const": "arbitrary unit", "type": "string" }, { "description": "An SI unit", "minLength": 1, "pattern": "^(Q|R|Y|Z|E|P|T|G|M|k|h|da|d|c|m|µ|n|p|f|a|z|y|r|q)?(m|g|s|A|K|mol|cd|Hz|N|Pa|J|W|C|V|F|Ω|S|Wb|T|H|lm|lx|Bq|Gy|Sv|kat|l|L)(\\^[+-]?[1-9]\\d*)?((·(Q|R|Y|Z|E|P|T|G|M|k|h|da|d|c|m|µ|n|p|f|a|z|y|r|q)?(m|g|s|A|K|mol|cd|Hz|N|Pa|J|W|C|V|F|Ω|S|Wb|T|H|lm|lx|Bq|Gy|Sv|kat|l|L)(\\^[+-]?[1-9]\\d*)?)|(/(Q|R|Y|Z|E|P|T|G|M|k|h|da|d|c|m|µ|n|p|f|a|z|y|r|q)?(m|g|s|A|K|mol|cd|Hz|N|Pa|J|W|C|V|F|Ω|S|Wb|T|H|lm|lx|Bq|Gy|Sv|kat|l|L)(\\^+?[1-9]\\d*)?))*$", "title": "SiUnit", "type": "string" } ], "default": "arbitrary unit", "title": "Unit" }, "scale": { "default": 1.0, "description": "Scale for data on an interval (or ratio) scale.", "title": "Scale", "type": "number" }, "offset": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Offset for data on a ratio scale.", "title": "Offset" } }, "title": "model.v0_5.IntervalOrRatioDataDescr", "additionalProperties": false }, "KerasV3WeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "Source of the .keras weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "keras_version": { "$ref": "#/$defs/Version", "description": "Keras version used to create these weights.", "ge": 3 }, "backend": { "description": "Keras backend used to create these weights.", "maxItems": 2, "minItems": 2, "prefixItems": [ { "enum": [ "tensorflow", "jax", "torch" ], "type": "string" }, { "$ref": "#/$defs/Version" } ], "title": "Backend", "type": "array" } }, "required": [ "source", "keras_version", "backend" ], "title": "model.v0_5.KerasV3WeightsDescr", "additionalProperties": false }, "NominalOrOrdinalDataDescr": { "type": "object", "properties": { "values": { "anyOf": [ { "items": { "type": "integer" }, "minItems": 1, "type": "array" }, { "items": { "type": "number" }, "minItems": 1, "type": "array" }, { "items": { "type": "boolean" }, "minItems": 1, "type": "array" }, { "items": { "type": "string" }, "minItems": 1, "type": "array" } ], "description": "A fixed set of nominal or an ascending sequence of ordinal values.\nIn this case `data.type` is required to be an unsigend integer type, e.g. 'uint8'.\nString `values` are interpreted as labels for tensor values 0, ..., N.\nNote: as YAML 1.2 does not natively support a \"set\" datatype,\nnominal values should be given as a sequence (aka list/array) as well.", "title": "Values" }, "type": { "default": "uint8", "enum": [ "float32", "float64", "uint8", "int8", "uint16", "int16", "uint32", "int32", "uint64", "int64", "bool" ], "examples": [ "float32", "uint8", "uint16", "int64", "bool" ], "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "const": "arbitrary unit", "type": "string" }, { "description": "An SI unit", "minLength": 1, "pattern": "^(Q|R|Y|Z|E|P|T|G|M|k|h|da|d|c|m|µ|n|p|f|a|z|y|r|q)?(m|g|s|A|K|mol|cd|Hz|N|Pa|J|W|C|V|F|Ω|S|Wb|T|H|lm|lx|Bq|Gy|Sv|kat|l|L)(\\^[+-]?[1-9]\\d*)?((·(Q|R|Y|Z|E|P|T|G|M|k|h|da|d|c|m|µ|n|p|f|a|z|y|r|q)?(m|g|s|A|K|mol|cd|Hz|N|Pa|J|W|C|V|F|Ω|S|Wb|T|H|lm|lx|Bq|Gy|Sv|kat|l|L)(\\^[+-]?[1-9]\\d*)?)|(/(Q|R|Y|Z|E|P|T|G|M|k|h|da|d|c|m|µ|n|p|f|a|z|y|r|q)?(m|g|s|A|K|mol|cd|Hz|N|Pa|J|W|C|V|F|Ω|S|Wb|T|H|lm|lx|Bq|Gy|Sv|kat|l|L)(\\^+?[1-9]\\d*)?))*$", "title": "SiUnit", "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" } }, "required": [ "values" ], "title": "model.v0_5.NominalOrOrdinalDataDescr", "additionalProperties": false }, "ParameterizedInputShape": { "type": "object", "description": "A sequence of valid shapes given by `shape_k = min + k * step for k in {0, 1, ...}`.", "properties": { "min": { "description": "The minimum input shape", "items": { "type": "integer" }, "minItems": 1, "title": "Min", "type": "array" }, "step": { "description": "The minimum shape change", "items": { "type": "integer" }, "minItems": 1, "title": "Step", "type": "array" } }, "required": [ "min", "step" ], "title": "model.v0_4.ParameterizedInputShape", "additionalProperties": false }, "ParameterizedSize": { "type": "object", "description": "Describes a range of valid tensor axis sizes as `size = min + n*step`.\n\n- **min** and **step** are given by the model description.\n- All blocksize paramters n = 0,1,2,... yield a valid `size`.\n- A greater blocksize paramter n = 0,1,2,... results in a greater **size**.\n This allows to adjust the axis size more generically.", "properties": { "min": { "exclusiveMinimum": 0, "title": "Min", "type": "integer" }, "step": { "exclusiveMinimum": 0, "title": "Step", "type": "integer" } }, "required": [ "min", "step" ], "title": "model.v0_5.ParameterizedSize", "additionalProperties": false }, "RelativeFilePath": { "description": "A path relative to the `rdf.yaml` file (also if the RDF source is a URL).", "format": "path", "title": "RelativeFilePath", "type": "string" }, "ReproducibilityTolerance": { "type": "object", "description": "Describes what small numerical differences -- if any -- may be tolerated\nin the generated output when executing in different environments.\n\nA tensor element *output* is considered mismatched to the **test_tensor** if\nabs(*output* - **test_tensor**) > **absolute_tolerance** + **relative_tolerance** * abs(**test_tensor**).\n(Internally we call [numpy.testing.assert_allclose](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_allclose.html).)\n\nMotivation:\n For testing we can request the respective deep learning frameworks to be as\n reproducible as possible by setting seeds and chosing deterministic algorithms,\n but differences in operating systems, available hardware and installed drivers\n may still lead to numerical differences.", "properties": { "relative_tolerance": { "default": 0.001, "description": "Maximum relative tolerance of reproduced test tensor.", "maximum": 0.01, "minimum": 0, "title": "Relative Tolerance", "type": "number" }, "absolute_tolerance": { "default": 0.001, "description": "Maximum absolute tolerance of reproduced test tensor.", "minimum": 0, "title": "Absolute Tolerance", "type": "number" }, "mismatched_elements_per_million": { "default": 100, "description": "Maximum number of mismatched elements/pixels per million to tolerate.", "maximum": 1000, "minimum": 0, "title": "Mismatched Elements Per Million", "type": "integer" }, "output_ids": { "default": [], "description": "Limits the output tensor IDs these reproducibility details apply to.", "items": { "maxLength": 32, "minLength": 1, "title": "TensorId", "type": "string" }, "title": "Output Ids", "type": "array" }, "weights_formats": { "default": [], "description": "Limits the weights formats these details apply to.", "items": { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, "title": "Weights Formats", "type": "array" } }, "title": "model.v0_5.ReproducibilityTolerance", "additionalProperties": true }, "RunMode": { "type": "object", "properties": { "name": { "anyOf": [ { "const": "deepimagej", "type": "string" }, { "type": "string" } ], "description": "Run mode name", "title": "Name" }, "kwargs": { "type": "object", "description": "Run mode specific key word arguments", "title": "Kwargs", "additionalProperties": true } }, "required": [ "name" ], "title": "model.v0_4.RunMode", "additionalProperties": false }, "ScaleLinearAlongAxisKwargs": { "type": "object", "description": "Key word arguments for `ScaleLinearDescr`", "properties": { "axis": { "description": "The axis of gain and offset values.", "examples": [ "channel" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "gain": { "anyOf": [ { "type": "number" }, { "items": { "type": "number" }, "minItems": 1, "type": "array" } ], "default": 1.0, "description": "multiplicative factor", "title": "Gain" }, "offset": { "anyOf": [ { "type": "number" }, { "items": { "type": "number" }, "minItems": 1, "type": "array" } ], "default": 0.0, "description": "additive term", "title": "Offset" } }, "required": [ "axis" ], "title": "model.v0_5.ScaleLinearAlongAxisKwargs", "additionalProperties": false }, "SizeReference": { "type": "object", "description": "A tensor axis size (extent in pixels/frames) defined in relation to a reference axis.\n\n`axis.size = reference.size * reference.scale / axis.scale + offset`\n\nNote:\n1. The axis and the referenced axis need to have the same unit (or no unit).\n2. Batch axes may not be referenced.\n3. Fractions are rounded down.\n4. If the reference axis is `concatenable` the referencing axis is assumed to be\n `concatenable` as well with the same block order.\n\nExample:\nAn unisotropic input image of w*h=100*49 pixels depicts a phsical space of 200*196mm².\nLet's assume that we want to express the image height h in relation to its width w\ninstead of only accepting input images of exactly 100*49 pixels\n(for example to express a range of valid image shapes by parametrizing w, see `ParameterizedSize`).\n\n>>> w = SpaceInputAxis(id=AxisId(\"w\"), size=100, unit=\"millimeter\", scale=2)\n>>> h = SpaceInputAxis(\n... id=AxisId(\"h\"),\n... size=SizeReference(tensor_id=TensorId(\"input\"), axis_id=AxisId(\"w\"), offset=-1),\n... unit=\"millimeter\",\n... scale=4,\n... )\n>>> print(h.size.get_size(h, w))\n49\n\n⇒ h = w * w.scale / h.scale + offset = 100 * 2mm / 4mm - 1 = 49", "properties": { "tensor_id": { "description": "tensor id of the reference axis", "maxLength": 32, "minLength": 1, "title": "TensorId", "type": "string" }, "axis_id": { "description": "axis id of the reference axis", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "offset": { "default": 0, "title": "Offset", "type": "integer" } }, "required": [ "tensor_id", "axis_id" ], "title": "model.v0_5.SizeReference", "additionalProperties": false }, "SoftmaxDescr": { "type": "object", "description": "The softmax function.\n\nExamples:\n- in YAML\n ```yaml\n postprocessing:\n - id: softmax\n kwargs:\n axis: channel\n ```\n- in Python:\n\n >>> postprocessing = [SoftmaxDescr(kwargs=SoftmaxKwargs(axis=AxisId(\"channel\")))]", "properties": { "id": { "const": "softmax", "title": "Id", "type": "string" }, "kwargs": { "$ref": "#/$defs/SoftmaxKwargs" } }, "required": [ "id" ], "title": "model.v0_5.SoftmaxDescr", "additionalProperties": false }, "SoftmaxKwargs": { "type": "object", "description": "key word arguments for `SoftmaxDescr`", "properties": { "axis": { "default": "channel", "description": "The axis to apply the softmax function along.\nNote:\n Defaults to 'channel' axis\n (which may not exist, in which case\n a different axis id has to be specified).", "examples": [ "channel" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" } }, "title": "model.v0_5.SoftmaxKwargs", "additionalProperties": false }, "SpaceInputAxis": { "type": "object", "properties": { "size": { "anyOf": [ { "exclusiveMinimum": 0, "type": "integer" }, { "$ref": "#/$defs/ParameterizedSize" }, { "$ref": "#/$defs/SizeReference" } ], "description": "The size/length of this axis can be specified as\n- fixed integer\n- parameterized series of valid sizes (`ParameterizedSize`)\n- reference to another axis with an optional offset (`SizeReference`)", "examples": [ 10, { "min": 32, "step": 16 }, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ], "title": "Size" }, "id": { "default": "x", "examples": [ "x", "y", "z" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "space", "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "enum": [ "attometer", "angstrom", "centimeter", "decimeter", "exameter", "femtometer", "foot", "gigameter", "hectometer", "inch", "kilometer", "megameter", "meter", "micrometer", "mile", "millimeter", "nanometer", "parsec", "petameter", "picometer", "terameter", "yard", "yoctometer", "yottameter", "zeptometer", "zettameter" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" }, "scale": { "default": 1.0, "exclusiveMinimum": 0, "title": "Scale", "type": "number" }, "concatenable": { "default": false, "description": "If a model has a `concatenable` input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a `SizeReference` to a concatenable\ninput axis.", "title": "Concatenable", "type": "boolean" } }, "required": [ "size", "type" ], "title": "model.v0_5.SpaceInputAxis", "additionalProperties": false }, "SpaceOutputAxis": { "type": "object", "properties": { "size": { "anyOf": [ { "exclusiveMinimum": 0, "type": "integer" }, { "$ref": "#/$defs/SizeReference" } ], "description": "The size/length of this axis can be specified as\n- fixed integer\n- reference to another axis with an optional offset (see `SizeReference`)", "examples": [ 10, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ], "title": "Size" }, "id": { "default": "x", "examples": [ "x", "y", "z" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "space", "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "enum": [ "attometer", "angstrom", "centimeter", "decimeter", "exameter", "femtometer", "foot", "gigameter", "hectometer", "inch", "kilometer", "megameter", "meter", "micrometer", "mile", "millimeter", "nanometer", "parsec", "petameter", "picometer", "terameter", "yard", "yoctometer", "yottameter", "zeptometer", "zettameter" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" }, "scale": { "default": 1.0, "exclusiveMinimum": 0, "title": "Scale", "type": "number" } }, "required": [ "size", "type" ], "title": "model.v0_5.SpaceOutputAxis", "additionalProperties": false }, "SpaceOutputAxisWithHalo": { "type": "object", "properties": { "halo": { "description": "The halo should be cropped from the output tensor to avoid boundary effects.\nIt is to be cropped from both sides, i.e. `size_after_crop = size - 2 * halo`.\nTo document a halo that is already cropped by the model use `size.offset` instead.", "minimum": 1, "title": "Halo", "type": "integer" }, "size": { "$ref": "#/$defs/SizeReference", "description": "reference to another axis with an optional offset (see `SizeReference`)", "examples": [ 10, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ] }, "id": { "default": "x", "examples": [ "x", "y", "z" ], "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "space", "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "enum": [ "attometer", "angstrom", "centimeter", "decimeter", "exameter", "femtometer", "foot", "gigameter", "hectometer", "inch", "kilometer", "megameter", "meter", "micrometer", "mile", "millimeter", "nanometer", "parsec", "petameter", "picometer", "terameter", "yard", "yoctometer", "yottameter", "zeptometer", "zettameter" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" }, "scale": { "default": 1.0, "exclusiveMinimum": 0, "title": "Scale", "type": "number" } }, "required": [ "halo", "size", "type" ], "title": "model.v0_5.SpaceOutputAxisWithHalo", "additionalProperties": false }, "StardistPostprocessingDescr": { "type": "object", "description": "Stardist postprocessing including non-maximum suppression and converting polygon representations to instance labels\n\nas described in:\n- Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers.\n[*Cell Detection with Star-convex Polygons*](https://arxiv.org/abs/1806.03535).\nInternational Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018.\n- Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, and Gene Myers.\n[*Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy*](http://openaccess.thecvf.com/content_WACV_2020/papers/Weigert_Star-convex_Polyhedra_for_3D_Object_Detection_and_Segmentation_in_Microscopy_WACV_2020_paper.pdf).\nThe IEEE Winter Conference on Applications of Computer Vision (WACV), Snowmass Village, Colorado, March 2020.\n\nNote: Only available if the `stardist` package is installed.", "properties": { "id": { "const": "stardist_postprocessing", "title": "Id", "type": "string" }, "kwargs": { "anyOf": [ { "$ref": "#/$defs/StardistPostprocessingKwargs2D" }, { "$ref": "#/$defs/StardistPostprocessingKwargs3D" } ], "title": "Kwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.StardistPostprocessingDescr", "additionalProperties": false }, "StardistPostprocessingKwargs2D": { "type": "object", "properties": { "prob_threshold": { "description": "The probability threshold for object candidate selection.", "title": "Prob Threshold", "type": "number" }, "nms_threshold": { "description": "The IoU threshold for non-maximum suppression.", "title": "Nms Threshold", "type": "number" }, "grid": { "description": "Grid size of network predictions.", "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "title": "Grid", "type": "array" }, "b": { "anyOf": [ { "type": "integer" }, { "maxItems": 2, "minItems": 2, "prefixItems": [ { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "type": "array" }, { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "type": "array" } ], "type": "array" } ], "description": "Border region in which object probability is set to zero.", "title": "B" } }, "required": [ "prob_threshold", "nms_threshold", "grid", "b" ], "title": "model.v0_5.StardistPostprocessingKwargs2D", "additionalProperties": false }, "StardistPostprocessingKwargs3D": { "type": "object", "properties": { "prob_threshold": { "description": "The probability threshold for object candidate selection.", "title": "Prob Threshold", "type": "number" }, "nms_threshold": { "description": "The IoU threshold for non-maximum suppression.", "title": "Nms Threshold", "type": "number" }, "grid": { "description": "Grid size of network predictions.", "maxItems": 3, "minItems": 3, "prefixItems": [ { "type": "integer" }, { "type": "integer" }, { "type": "integer" } ], "title": "Grid", "type": "array" }, "b": { "anyOf": [ { "type": "integer" }, { "maxItems": 3, "minItems": 3, "prefixItems": [ { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "type": "array" }, { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "type": "array" }, { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "integer" }, { "type": "integer" } ], "type": "array" } ], "type": "array" } ], "description": "Border region in which object probability is set to zero.", "title": "B" }, "n_rays": { "description": "Number of rays for 3D star-convex polyhedra.", "title": "N Rays", "type": "integer" }, "anisotropy": { "description": "Anisotropy factors for 3D star-convex polyhedra, i.e. the physical pixel size along each spatial axis.", "maxItems": 3, "minItems": 3, "prefixItems": [ { "type": "number" }, { "type": "number" }, { "type": "number" } ], "title": "Anisotropy", "type": "array" }, "overlap_label": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "Optional label to apply to any area of overlapping predicted objects.", "title": "Overlap Label" } }, "required": [ "prob_threshold", "nms_threshold", "grid", "b", "n_rays", "anisotropy" ], "title": "model.v0_5.StardistPostprocessingKwargs3D", "additionalProperties": false }, "TimeInputAxis": { "type": "object", "properties": { "size": { "anyOf": [ { "exclusiveMinimum": 0, "type": "integer" }, { "$ref": "#/$defs/ParameterizedSize" }, { "$ref": "#/$defs/SizeReference" } ], "description": "The size/length of this axis can be specified as\n- fixed integer\n- parameterized series of valid sizes (`ParameterizedSize`)\n- reference to another axis with an optional offset (`SizeReference`)", "examples": [ 10, { "min": 32, "step": 16 }, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ], "title": "Size" }, "id": { "default": "time", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "time", "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "enum": [ "attosecond", "centisecond", "day", "decisecond", "exasecond", "femtosecond", "gigasecond", "hectosecond", "hour", "kilosecond", "megasecond", "microsecond", "millisecond", "minute", "nanosecond", "petasecond", "picosecond", "second", "terasecond", "yoctosecond", "yottasecond", "zeptosecond", "zettasecond" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" }, "scale": { "default": 1.0, "exclusiveMinimum": 0, "title": "Scale", "type": "number" }, "concatenable": { "default": false, "description": "If a model has a `concatenable` input axis, it can be processed blockwise,\nsplitting a longer sample axis into blocks matching its input tensor description.\nOutput axes are concatenable if they have a `SizeReference` to a concatenable\ninput axis.", "title": "Concatenable", "type": "boolean" } }, "required": [ "size", "type" ], "title": "model.v0_5.TimeInputAxis", "additionalProperties": false }, "TimeOutputAxis": { "type": "object", "properties": { "size": { "anyOf": [ { "exclusiveMinimum": 0, "type": "integer" }, { "$ref": "#/$defs/SizeReference" } ], "description": "The size/length of this axis can be specified as\n- fixed integer\n- reference to another axis with an optional offset (see `SizeReference`)", "examples": [ 10, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ], "title": "Size" }, "id": { "default": "time", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "time", "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "enum": [ "attosecond", "centisecond", "day", "decisecond", "exasecond", "femtosecond", "gigasecond", "hectosecond", "hour", "kilosecond", "megasecond", "microsecond", "millisecond", "minute", "nanosecond", "petasecond", "picosecond", "second", "terasecond", "yoctosecond", "yottasecond", "zeptosecond", "zettasecond" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" }, "scale": { "default": 1.0, "exclusiveMinimum": 0, "title": "Scale", "type": "number" } }, "required": [ "size", "type" ], "title": "model.v0_5.TimeOutputAxis", "additionalProperties": false }, "TimeOutputAxisWithHalo": { "type": "object", "properties": { "halo": { "description": "The halo should be cropped from the output tensor to avoid boundary effects.\nIt is to be cropped from both sides, i.e. `size_after_crop = size - 2 * halo`.\nTo document a halo that is already cropped by the model use `size.offset` instead.", "minimum": 1, "title": "Halo", "type": "integer" }, "size": { "$ref": "#/$defs/SizeReference", "description": "reference to another axis with an optional offset (see `SizeReference`)", "examples": [ 10, { "axis_id": "a", "offset": 5, "tensor_id": "t" } ] }, "id": { "default": "time", "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "description": { "default": "", "description": "A short description of this axis beyond its type and id.", "maxLength": 128, "title": "Description", "type": "string" }, "type": { "const": "time", "title": "Type", "type": "string" }, "unit": { "anyOf": [ { "enum": [ "attosecond", "centisecond", "day", "decisecond", "exasecond", "femtosecond", "gigasecond", "hectosecond", "hour", "kilosecond", "megasecond", "microsecond", "millisecond", "minute", "nanosecond", "petasecond", "picosecond", "second", "terasecond", "yoctosecond", "yottasecond", "zeptosecond", "zettasecond" ], "type": "string" }, { "type": "null" } ], "default": null, "title": "Unit" }, "scale": { "default": 1.0, "exclusiveMinimum": 0, "title": "Scale", "type": "number" } }, "required": [ "halo", "size", "type" ], "title": "model.v0_5.TimeOutputAxisWithHalo", "additionalProperties": false }, "TrainingDetails": { "type": "object", "properties": { "training_preprocessing": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Detailed image preprocessing steps during model training:\n\nMention:\n- *Normalization methods*\n- *Augmentation strategies*\n- *Resizing/resampling procedures*\n- *Artifact handling*", "title": "Training Preprocessing" }, "training_epochs": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Number of training epochs.", "title": "Training Epochs" }, "training_batch_size": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Batch size used in training.", "title": "Training Batch Size" }, "initial_learning_rate": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Initial learning rate used in training.", "title": "Initial Learning Rate" }, "learning_rate_schedule": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Learning rate schedule used in training.", "title": "Learning Rate Schedule" }, "loss_function": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Loss function used in training, e.g. nn.MSELoss.", "title": "Loss Function" }, "loss_function_kwargs": { "type": "object", "description": "key word arguments for the `loss_function`", "title": "Loss Function Kwargs", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "optimizer": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "optimizer, e.g. torch.optim.Adam", "title": "Optimizer" }, "optimizer_kwargs": { "type": "object", "description": "key word arguments for the `optimizer`", "title": "Optimizer Kwargs", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "regularization": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Regularization techniques used during training, e.g. drop-out or weight decay.", "title": "Regularization" }, "training_duration": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Total training duration in hours.", "title": "Training Duration" } }, "title": "model.v0_5.TrainingDetails", "additionalProperties": true }, "Uploader": { "type": "object", "properties": { "email": { "description": "Email", "format": "email", "title": "Email", "type": "string" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "name", "title": "Name" } }, "required": [ "email" ], "title": "generic.v0_2.Uploader", "additionalProperties": false }, "Version": { "anyOf": [ { "type": "string" }, { "type": "integer" }, { "type": "number" } ], "description": "wraps a packaging.version.Version instance for validation in pydantic models", "title": "Version" }, "YamlValue": { "anyOf": [ { "type": "boolean" }, { "format": "date", "type": "string" }, { "format": "date-time", "type": "string" }, { "type": "integer" }, { "type": "number" }, { "type": "string" }, { "items": { "$ref": "#/$defs/YamlValue" }, "type": "array" }, { "type": "object", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, { "type": "null" } ] }, "bioimageio__spec__application__v0_2__ApplicationDescr": { "type": "object", "description": "Bioimage.io description of an application.", "properties": { "name": { "description": "A human-friendly name of the resource description", "minLength": 1, "title": "Name", "type": "string" }, "description": { "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 1, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of the RDF and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "title": "Authors", "type": "array" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "file and other attachments" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__CiteEntry" }, "title": "Cite", "type": "array" }, "config": { "type": "object", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)", "examples": [ { "bioimageio": { "another_key": { "nested": "value" }, "my_custom_key": 3837283 }, "imagej": { "macro_dir": "path/to/macro/file" } } ], "title": "Config", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "download_url": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL to download the resource from (deprecated)", "title": "Download Url" }, "git_repo": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Maintainer" }, "title": "Maintainers", "type": "array" }, "rdf_source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.", "title": "Rdf Source" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_number": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "version number (n-th published version, not the semantic version)", "title": "Version Number" }, "format_version": { "const": "0.2.4", "description": "The format version of this resource specification\n(not the `version` of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.", "title": "Format Version", "type": "string" }, "badges": { "description": "badges associated with this resource", "items": { "$ref": "#/$defs/BadgeDescr" }, "title": "Badges", "type": "array" }, "documentation": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.", "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ], "title": "Documentation" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "type": { "const": "application", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "ApplicationId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL or path to the source of the application", "title": "Source" } }, "required": [ "name", "description", "format_version", "type" ], "title": "application 0.2.4", "additionalProperties": false }, "bioimageio__spec__application__v0_3__ApplicationDescr": { "type": "object", "description": "Bioimage.io description of an application.", "properties": { "name": { "description": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.", "maxLength": 128, "minLength": 5, "title": "Name", "type": "string" }, "description": { "default": "", "description": "A string containing a brief description.", "maxLength": 1024, "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 2, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of this resource description and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "title": "Authors", "type": "array" }, "attachments": { "description": "file attachments", "items": { "$ref": "#/$defs/FileDescr" }, "title": "Attachments", "type": "array" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__CiteEntry" }, "title": "Cite", "type": "array" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose)\nto discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "git_repo": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration, e.g. on bioimage.io", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified, `authors` are maintainers and at least some of them has to specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Maintainer" }, "title": "Maintainers", "type": "array" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_comment": { "anyOf": [ { "maxLength": 512, "type": "string" }, { "type": "null" } ], "default": null, "description": "A comment on the version of the resource.", "title": "Version Comment" }, "format_version": { "const": "0.3.0", "description": "The **format** version of this resource specification", "title": "Format Version", "type": "string" }, "documentation": { "anyOf": [ { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ] }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.", "title": "Documentation" }, "badges": { "description": "badges associated with this resource", "items": { "$ref": "#/$defs/BadgeDescr" }, "title": "Badges", "type": "array" }, "config": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Config", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a GitHub repo URL in `config` since there is a `git_repo` field.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n giraffe_neckometer: # here is the domain name\n length: 3837283\n address:\n home: zoo\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource.\n(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files.)" }, "type": { "const": "application", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "ApplicationId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "parent": { "anyOf": [ { "minLength": 1, "title": "ApplicationId", "type": "string" }, { "type": "null" } ], "default": null, "description": "The description from which this one is derived", "title": "Parent" }, "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL or path to the source of the application", "title": "Source" } }, "required": [ "name", "format_version", "type" ], "title": "application 0.3.0", "additionalProperties": false }, "bioimageio__spec__dataset__v0_2__DatasetDescr": { "type": "object", "description": "A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.", "properties": { "name": { "description": "A human-friendly name of the resource description", "minLength": 1, "title": "Name", "type": "string" }, "description": { "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 1, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of the RDF and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "title": "Authors", "type": "array" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "file and other attachments" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__CiteEntry" }, "title": "Cite", "type": "array" }, "config": { "type": "object", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)", "examples": [ { "bioimageio": { "another_key": { "nested": "value" }, "my_custom_key": 3837283 }, "imagej": { "macro_dir": "path/to/macro/file" } } ], "title": "Config", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "download_url": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL to download the resource from (deprecated)", "title": "Download Url" }, "git_repo": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Maintainer" }, "title": "Maintainers", "type": "array" }, "rdf_source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.", "title": "Rdf Source" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_number": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "version number (n-th published version, not the semantic version)", "title": "Version Number" }, "format_version": { "const": "0.2.4", "description": "The format version of this resource specification\n(not the `version` of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.", "title": "Format Version", "type": "string" }, "badges": { "description": "badges associated with this resource", "items": { "$ref": "#/$defs/BadgeDescr" }, "title": "Badges", "type": "array" }, "documentation": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.", "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ], "title": "Documentation" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "type": { "const": "dataset", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "DatasetId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "\"URL to the source of the dataset.", "title": "Source" } }, "required": [ "name", "description", "format_version", "type" ], "title": "dataset 0.2.4", "additionalProperties": false }, "bioimageio__spec__dataset__v0_2__LinkedDataset": { "type": "object", "description": "Reference to a bioimage.io dataset.", "properties": { "id": { "description": "A valid dataset `id` from the bioimage.io collection.", "minLength": 1, "title": "DatasetId", "type": "string" }, "version_number": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "version number (n-th published version, not the semantic version) of linked dataset", "title": "Version Number" } }, "required": [ "id" ], "title": "dataset.v0_2.LinkedDataset", "additionalProperties": false }, "bioimageio__spec__dataset__v0_3__DatasetDescr": { "type": "object", "description": "A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage\nprocessing.", "properties": { "name": { "description": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.", "maxLength": 128, "minLength": 5, "title": "Name", "type": "string" }, "description": { "default": "", "description": "A string containing a brief description.", "maxLength": 1024, "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 2, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of this resource description and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "title": "Authors", "type": "array" }, "attachments": { "description": "file attachments", "items": { "$ref": "#/$defs/FileDescr" }, "title": "Attachments", "type": "array" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__CiteEntry" }, "title": "Cite", "type": "array" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose)\nto discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "git_repo": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration, e.g. on bioimage.io", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified, `authors` are maintainers and at least some of them has to specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Maintainer" }, "title": "Maintainers", "type": "array" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_comment": { "anyOf": [ { "maxLength": 512, "type": "string" }, { "type": "null" } ], "default": null, "description": "A comment on the version of the resource.", "title": "Version Comment" }, "format_version": { "const": "0.3.0", "description": "The **format** version of this resource specification", "title": "Format Version", "type": "string" }, "documentation": { "anyOf": [ { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ] }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.", "title": "Documentation" }, "badges": { "description": "badges associated with this resource", "items": { "$ref": "#/$defs/BadgeDescr" }, "title": "Badges", "type": "array" }, "config": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Config", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a GitHub repo URL in `config` since there is a `git_repo` field.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n giraffe_neckometer: # here is the domain name\n length: 3837283\n address:\n home: zoo\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource.\n(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files.)" }, "type": { "const": "dataset", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "DatasetId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "parent": { "anyOf": [ { "minLength": 1, "title": "DatasetId", "type": "string" }, { "type": "null" } ], "default": null, "description": "The description from which this one is derived", "title": "Parent" }, "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "\"URL to the source of the dataset.", "title": "Source" } }, "required": [ "name", "format_version", "type" ], "title": "dataset 0.3.0", "additionalProperties": false }, "bioimageio__spec__dataset__v0_3__LinkedDataset": { "type": "object", "description": "Reference to a bioimage.io dataset.", "properties": { "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the linked resource following SemVer 2.0." }, "id": { "description": "A valid dataset `id` from the bioimage.io collection.", "minLength": 1, "title": "DatasetId", "type": "string" } }, "required": [ "id" ], "title": "dataset.v0_3.LinkedDataset", "additionalProperties": false }, "bioimageio__spec__generic__v0_2__Author": { "type": "object", "properties": { "affiliation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Affiliation", "title": "Affiliation" }, "email": { "anyOf": [ { "format": "email", "type": "string" }, { "type": "null" } ], "default": null, "description": "Email", "title": "Email" }, "orcid": { "anyOf": [ { "description": "An ORCID identifier, see ", "title": "OrcidId", "type": "string" }, { "type": "null" } ], "default": null, "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\n\n) as per ISO 7064 11,2.)", "examples": [ "0000-0001-2345-6789" ], "title": "Orcid" }, "name": { "title": "Name", "type": "string" }, "github_user": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Github User" } }, "required": [ "name" ], "title": "generic.v0_2.Author", "additionalProperties": false }, "bioimageio__spec__generic__v0_2__CiteEntry": { "type": "object", "properties": { "text": { "description": "free text description", "title": "Text", "type": "string" }, "doi": { "anyOf": [ { "description": "A digital object identifier, see ", "pattern": "^10\\.[0-9]{4}.+$", "title": "Doi", "type": "string" }, { "type": "null" } ], "default": null, "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee for details. (alternatively specify `url`)", "title": "Doi" }, "url": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "URL to cite (preferably specify a `doi` instead)", "title": "Url" } }, "required": [ "text" ], "title": "generic.v0_2.CiteEntry", "additionalProperties": false }, "bioimageio__spec__generic__v0_2__Maintainer": { "type": "object", "properties": { "affiliation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Affiliation", "title": "Affiliation" }, "email": { "anyOf": [ { "format": "email", "type": "string" }, { "type": "null" } ], "default": null, "description": "Email", "title": "Email" }, "orcid": { "anyOf": [ { "description": "An ORCID identifier, see ", "title": "OrcidId", "type": "string" }, { "type": "null" } ], "default": null, "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\n\n) as per ISO 7064 11,2.)", "examples": [ "0000-0001-2345-6789" ], "title": "Orcid" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "github_user": { "title": "Github User", "type": "string" } }, "required": [ "github_user" ], "title": "generic.v0_2.Maintainer", "additionalProperties": false }, "bioimageio__spec__generic__v0_3__Author": { "type": "object", "properties": { "affiliation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Affiliation", "title": "Affiliation" }, "email": { "anyOf": [ { "format": "email", "type": "string" }, { "type": "null" } ], "default": null, "description": "Email", "title": "Email" }, "orcid": { "anyOf": [ { "description": "An ORCID identifier, see ", "title": "OrcidId", "type": "string" }, { "type": "null" } ], "default": null, "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\n\n) as per ISO 7064 11,2.)", "examples": [ "0000-0001-2345-6789" ], "title": "Orcid" }, "name": { "title": "Name", "type": "string" }, "github_user": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Github User" } }, "required": [ "name" ], "title": "generic.v0_3.Author", "additionalProperties": false }, "bioimageio__spec__generic__v0_3__BioimageioConfig": { "type": "object", "description": "bioimage.io internal metadata.", "properties": {}, "title": "generic.v0_3.BioimageioConfig", "additionalProperties": true }, "bioimageio__spec__generic__v0_3__CiteEntry": { "type": "object", "description": "A citation that should be referenced in work using this resource.", "properties": { "text": { "description": "free text description", "title": "Text", "type": "string" }, "doi": { "anyOf": [ { "description": "A digital object identifier, see ", "pattern": "^10\\.[0-9]{4}.+$", "title": "Doi", "type": "string" }, { "type": "null" } ], "default": null, "description": "A digital object identifier (DOI) is the prefered citation reference.\nSee for details.\nNote:\n Either **doi** or **url** have to be specified.", "title": "Doi" }, "url": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL to cite (preferably specify a **doi** instead/also).\nNote:\n Either **doi** or **url** have to be specified.", "title": "Url" } }, "required": [ "text" ], "title": "generic.v0_3.CiteEntry", "additionalProperties": false }, "bioimageio__spec__generic__v0_3__Config": { "type": "object", "description": "A place to store additional metadata (often tool specific).\n\nSuch additional metadata is typically set programmatically by the respective tool\nor by people with specific insights into the tool.\nIf you want to store additional metadata that does not match any of the other\nfields, think of a key unlikely to collide with anyone elses use-case/tool and save\nit here.\n\nPlease consider creating [an issue in the bioimageio.spec repository](https://github.com/bioimage-io/spec-bioimage-io/issues/new?template=Blank+issue)\nif you are not sure if an existing field could cover your use case\nor if you think such a field should exist.", "properties": { "bioimageio": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__BioimageioConfig" } }, "title": "generic.v0_3.Config", "additionalProperties": true }, "bioimageio__spec__generic__v0_3__Maintainer": { "type": "object", "properties": { "affiliation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Affiliation", "title": "Affiliation" }, "email": { "anyOf": [ { "format": "email", "type": "string" }, { "type": "null" } ], "default": null, "description": "Email", "title": "Email" }, "orcid": { "anyOf": [ { "description": "An ORCID identifier, see ", "title": "OrcidId", "type": "string" }, { "type": "null" } ], "default": null, "description": "An [ORCID iD](https://support.orcid.org/hc/en-us/sections/360001495313-What-is-ORCID\n) in hyphenated groups of 4 digits, (and [valid](\n\n) as per ISO 7064 11,2.)", "examples": [ "0000-0001-2345-6789" ], "title": "Orcid" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Name" }, "github_user": { "title": "Github User", "type": "string" } }, "required": [ "github_user" ], "title": "generic.v0_3.Maintainer", "additionalProperties": false }, "bioimageio__spec__model__v0_4__BinarizeDescr": { "type": "object", "description": "BinarizeDescr the tensor with a fixed `BinarizeKwargs.threshold`.\nValues above the threshold will be set to one, values below the threshold to zero.", "properties": { "name": { "const": "binarize", "title": "Name", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__BinarizeKwargs" } }, "required": [ "name", "kwargs" ], "title": "model.v0_4.BinarizeDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__BinarizeKwargs": { "type": "object", "description": "key word arguments for `BinarizeDescr`", "properties": { "threshold": { "description": "The fixed threshold", "title": "Threshold", "type": "number" } }, "required": [ "threshold" ], "title": "model.v0_4.BinarizeKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ClipDescr": { "type": "object", "description": "Clip tensor values to a range.\n\nSet tensor values below `ClipKwargs.min` to `ClipKwargs.min`\nand above `ClipKwargs.max` to `ClipKwargs.max`.", "properties": { "name": { "const": "clip", "title": "Name", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ClipKwargs" } }, "required": [ "name", "kwargs" ], "title": "model.v0_4.ClipDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ClipKwargs": { "type": "object", "description": "key word arguments for `ClipDescr`", "properties": { "min": { "description": "minimum value for clipping", "title": "Min", "type": "number" }, "max": { "description": "maximum value for clipping", "title": "Max", "type": "number" } }, "required": [ "min", "max" ], "title": "model.v0_4.ClipKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_4__InputTensorDescr": { "type": "object", "properties": { "name": { "description": "Tensor name. No duplicates are allowed.", "minLength": 1, "title": "TensorName", "type": "string" }, "description": { "default": "", "title": "Description", "type": "string" }, "axes": { "description": "Axes identifying characters. Same length and order as the axes in `shape`.\n| axis | description |\n| --- | --- |\n| b | batch (groups multiple samples) |\n| i | instance/index/element |\n| t | time |\n| c | channel |\n| z | spatial dimension z |\n| y | spatial dimension y |\n| x | spatial dimension x |", "title": "Axes", "type": "string" }, "data_range": { "anyOf": [ { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "number" }, { "type": "number" } ], "type": "array" }, { "type": "null" } ], "default": null, "description": "Tuple `(minimum, maximum)` specifying the allowed range of the data in this tensor.\nIf not specified, the full data range that can be expressed in `data_type` is allowed.", "title": "Data Range" }, "data_type": { "description": "For now an input tensor is expected to be given as `float32`.\nThe data flow in bioimage.io models is explained\n[in this diagram.](https://docs.google.com/drawings/d/1FTw8-Rn6a6nXdkZ_SkMumtcjvur9mtIhRqLwnKqZNHM/edit).", "enum": [ "float32", "uint8", "uint16" ], "title": "Data Type", "type": "string" }, "shape": { "anyOf": [ { "items": { "type": "integer" }, "type": "array" }, { "$ref": "#/$defs/ParameterizedInputShape" } ], "description": "Specification of input tensor shape.", "examples": [ [ 1, 512, 512, 1 ], { "min": [ 1, 64, 64, 1 ], "step": [ 0, 32, 32, 0 ] } ], "title": "Shape" }, "preprocessing": { "description": "Description of how this input should be preprocessed.", "items": { "discriminator": { "mapping": { "binarize": "#/$defs/bioimageio__spec__model__v0_4__BinarizeDescr", "clip": "#/$defs/bioimageio__spec__model__v0_4__ClipDescr", "scale_linear": "#/$defs/bioimageio__spec__model__v0_4__ScaleLinearDescr", "scale_range": "#/$defs/bioimageio__spec__model__v0_4__ScaleRangeDescr", "sigmoid": "#/$defs/bioimageio__spec__model__v0_4__SigmoidDescr", "zero_mean_unit_variance": "#/$defs/bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceDescr" }, "propertyName": "name" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__BinarizeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ClipDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleLinearDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__SigmoidDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleRangeDescr" } ] }, "title": "Preprocessing", "type": "array" } }, "required": [ "name", "axes", "data_type", "shape" ], "title": "model.v0_4.InputTensorDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__KerasHdf5WeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "Attachments that are specific to this weights entry." }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "dependencies": { "anyOf": [ { "pattern": "^.+:.+$", "title": "Dependencies", "type": "string" }, { "type": "null" } ], "default": null, "description": "Dependency manager and dependency file, specified as `:`.", "examples": [ "conda:environment.yaml", "maven:./pom.xml", "pip:./requirements.txt" ], "title": "Dependencies" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "tensorflow_version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "TensorFlow version used to create these weights" } }, "required": [ "source" ], "title": "model.v0_4.KerasHdf5WeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__LinkedModel": { "type": "object", "description": "Reference to a bioimage.io model.", "properties": { "id": { "description": "A valid model `id` from the bioimage.io collection.", "examples": [ "affable-shark", "ambitious-sloth" ], "minLength": 1, "title": "ModelId", "type": "string" }, "version_number": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "version number (n-th published version, not the semantic version) of linked model", "title": "Version Number" } }, "required": [ "id" ], "title": "model.v0_4.LinkedModel", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ModelDescr": { "type": "object", "description": "Specification of the fields used in a bioimage.io-compliant RDF that describes AI models with pretrained weights.\n\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).", "properties": { "name": { "description": "A human-readable name of this model.\nIt should be no longer than 64 characters and only contain letter, number, underscore, minus or space characters.", "minLength": 1, "title": "Name", "type": "string" }, "description": { "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 1, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of the model RDF and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "minItems": 1, "title": "Authors", "type": "array" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "file and other attachments" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__CiteEntry" }, "title": "Cite", "type": "array" }, "config": { "type": "object", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)", "examples": [ { "bioimageio": { "another_key": { "nested": "value" }, "my_custom_key": 3837283 }, "imagej": { "macro_dir": "path/to/macro/file" } } ], "title": "Config", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "download_url": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL to download the resource from (deprecated)", "title": "Download Url" }, "git_repo": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Maintainer" }, "title": "Maintainers", "type": "array" }, "rdf_source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.", "title": "Rdf Source" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_number": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "version number (n-th published version, not the semantic version)", "title": "Version Number" }, "format_version": { "const": "0.4.10", "description": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.", "title": "Format Version", "type": "string" }, "type": { "const": "model", "description": "Specialized resource type 'model'", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "ModelId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "documentation": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.\nThe documentation should include a '[#[#]]# Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.", "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ], "title": "Documentation" }, "inputs": { "description": "Describes the input tensors expected by this model.", "items": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__InputTensorDescr" }, "minItems": 1, "title": "Inputs", "type": "array" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "type": "string" } ], "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do notsupport custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "outputs": { "description": "Describes the output tensors.", "items": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__OutputTensorDescr" }, "minItems": 1, "title": "Outputs", "type": "array" }, "packaged_by": { "description": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the `authors`.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "title": "Packaged By", "type": "array" }, "parent": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__LinkedModel" }, { "type": "null" } ], "default": null, "description": "The model from which this model is derived, e.g. by fine-tuning the weights." }, "run_mode": { "anyOf": [ { "$ref": "#/$defs/RunMode" }, { "type": "null" } ], "default": null, "description": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet." }, "sample_inputs": { "description": "URLs/relative paths to sample inputs to illustrate possible inputs for the model,\nfor example stored as PNG or TIFF images.\nThe sample files primarily serve to inform a human user about an example use case", "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Sample Inputs", "type": "array" }, "sample_outputs": { "description": "URLs/relative paths to sample outputs corresponding to the `sample_inputs`.", "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Sample Outputs", "type": "array" }, "test_inputs": { "description": "Test input tensors compatible with the `inputs` description for a **single test case**.\nThis means if your model has more than one input, you should provide one URL/relative path for each input.\nEach test input should be a file with an ndarray in\n[numpy.lib file format](https://numpy.org/doc/stable/reference/generated/numpy.lib.format.html#module-numpy.lib.format).\nThe extension must be '.npy'.", "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "minItems": 1, "title": "Test Inputs", "type": "array" }, "test_outputs": { "description": "Analog to `test_inputs`.", "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "minItems": 1, "title": "Test Outputs", "type": "array" }, "timestamp": { "$ref": "#/$defs/Datetime" }, "training_data": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__dataset__v0_2__LinkedDataset" }, { "$ref": "#/$defs/bioimageio__spec__dataset__v0_2__DatasetDescr" }, { "type": "null" } ], "default": null, "description": "The dataset used to train this model", "title": "Training Data" }, "weights": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__WeightsDescr", "description": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model." } }, "required": [ "name", "description", "authors", "format_version", "type", "documentation", "inputs", "license", "outputs", "test_inputs", "test_outputs", "timestamp", "weights" ], "title": "model 0.4.10", "additionalProperties": false }, "bioimageio__spec__model__v0_4__OnnxWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "Attachments that are specific to this weights entry." }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "dependencies": { "anyOf": [ { "pattern": "^.+:.+$", "title": "Dependencies", "type": "string" }, { "type": "null" } ], "default": null, "description": "Dependency manager and dependency file, specified as `:`.", "examples": [ "conda:environment.yaml", "maven:./pom.xml", "pip:./requirements.txt" ], "title": "Dependencies" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "opset_version": { "anyOf": [ { "minimum": 7, "type": "integer" }, { "type": "null" } ], "default": null, "description": "ONNX opset version", "title": "Opset Version" } }, "required": [ "source" ], "title": "model.v0_4.OnnxWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__OutputTensorDescr": { "type": "object", "properties": { "name": { "description": "Tensor name. No duplicates are allowed.", "minLength": 1, "title": "TensorName", "type": "string" }, "description": { "default": "", "title": "Description", "type": "string" }, "axes": { "description": "Axes identifying characters. Same length and order as the axes in `shape`.\n| axis | description |\n| --- | --- |\n| b | batch (groups multiple samples) |\n| i | instance/index/element |\n| t | time |\n| c | channel |\n| z | spatial dimension z |\n| y | spatial dimension y |\n| x | spatial dimension x |", "title": "Axes", "type": "string" }, "data_range": { "anyOf": [ { "maxItems": 2, "minItems": 2, "prefixItems": [ { "type": "number" }, { "type": "number" } ], "type": "array" }, { "type": "null" } ], "default": null, "description": "Tuple `(minimum, maximum)` specifying the allowed range of the data in this tensor.\nIf not specified, the full data range that can be expressed in `data_type` is allowed.", "title": "Data Range" }, "data_type": { "description": "Data type.\nThe data flow in bioimage.io models is explained\n[in this diagram.](https://docs.google.com/drawings/d/1FTw8-Rn6a6nXdkZ_SkMumtcjvur9mtIhRqLwnKqZNHM/edit).", "enum": [ "float32", "float64", "uint8", "int8", "uint16", "int16", "uint32", "int32", "uint64", "int64", "bool" ], "title": "Data Type", "type": "string" }, "shape": { "anyOf": [ { "items": { "type": "integer" }, "type": "array" }, { "$ref": "#/$defs/ImplicitOutputShape" } ], "description": "Output tensor shape.", "title": "Shape" }, "halo": { "anyOf": [ { "items": { "type": "integer" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The `halo` that should be cropped from the output tensor to avoid boundary effects.\nThe `halo` is to be cropped from both sides, i.e. `shape_after_crop = shape - 2 * halo`.\nTo document a `halo` that is already cropped by the model `shape.offset` has to be used instead.", "title": "Halo" }, "postprocessing": { "description": "Description of how this output should be postprocessed.", "items": { "discriminator": { "mapping": { "binarize": "#/$defs/bioimageio__spec__model__v0_4__BinarizeDescr", "clip": "#/$defs/bioimageio__spec__model__v0_4__ClipDescr", "scale_linear": "#/$defs/bioimageio__spec__model__v0_4__ScaleLinearDescr", "scale_mean_variance": "#/$defs/bioimageio__spec__model__v0_4__ScaleMeanVarianceDescr", "scale_range": "#/$defs/bioimageio__spec__model__v0_4__ScaleRangeDescr", "sigmoid": "#/$defs/bioimageio__spec__model__v0_4__SigmoidDescr", "zero_mean_unit_variance": "#/$defs/bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceDescr" }, "propertyName": "name" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__BinarizeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ClipDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleLinearDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__SigmoidDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleRangeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleMeanVarianceDescr" } ] }, "title": "Postprocessing", "type": "array" } }, "required": [ "name", "axes", "data_type", "shape" ], "title": "model.v0_4.OutputTensorDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__PytorchStateDictWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "Attachments that are specific to this weights entry." }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "dependencies": { "anyOf": [ { "pattern": "^.+:.+$", "title": "Dependencies", "type": "string" }, { "type": "null" } ], "default": null, "description": "Dependency manager and dependency file, specified as `:`.", "examples": [ "conda:environment.yaml", "maven:./pom.xml", "pip:./requirements.txt" ], "title": "Dependencies" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "architecture": { "anyOf": [ { "pattern": "^.+:.+$", "title": "CallableFromFile", "type": "string" }, { "pattern": "^.+\\..+$", "title": "CallableFromDepencency", "type": "string" } ], "description": "callable returning a torch.nn.Module instance.\nLocal implementation: `:`.\nImplementation in a dependency: `.<[dependency-module]>.`.", "examples": [ "my_function.py:MyNetworkClass", "my_module.submodule.get_my_model" ], "title": "Architecture" }, "architecture_sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "The SHA256 of the architecture source file, if the architecture is not defined in a module listed in `dependencies`\nYou can drag and drop your file to this\n[online tool](http://emn178.github.io/online-tools/sha256_checksum.html) to generate a SHA256 in your browser.\nOr you can generate a SHA256 checksum with Python's `hashlib`,\n[here is a codesnippet](https://gist.github.com/FynnBe/e64460463df89439cff218bbf59c1100).", "title": "Architecture Sha256" }, "kwargs": { "type": "object", "description": "key word arguments for the `architecture` callable", "title": "Kwargs", "additionalProperties": true }, "pytorch_version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "Version of the PyTorch library used.\nIf `depencencies` is specified it should include pytorch and the verison has to match.\n(`dependencies` overrules `pytorch_version`)" } }, "required": [ "source", "architecture" ], "title": "model.v0_4.PytorchStateDictWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ScaleLinearDescr": { "type": "object", "description": "Fixed linear scaling.", "properties": { "name": { "const": "scale_linear", "title": "Name", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleLinearKwargs" } }, "required": [ "name", "kwargs" ], "title": "model.v0_4.ScaleLinearDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ScaleLinearKwargs": { "type": "object", "description": "key word arguments for `ScaleLinearDescr`", "properties": { "axes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "The subset of axes to scale jointly.\nFor example xy to scale the two image axes for 2d data jointly.", "examples": [ "xy" ], "title": "Axes" }, "gain": { "anyOf": [ { "type": "number" }, { "items": { "type": "number" }, "type": "array" } ], "default": 1.0, "description": "multiplicative factor", "title": "Gain" }, "offset": { "anyOf": [ { "type": "number" }, { "items": { "type": "number" }, "type": "array" } ], "default": 0.0, "description": "additive term", "title": "Offset" } }, "title": "model.v0_4.ScaleLinearKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ScaleMeanVarianceDescr": { "type": "object", "description": "Scale the tensor s.t. its mean and variance match a reference tensor.", "properties": { "name": { "const": "scale_mean_variance", "title": "Name", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleMeanVarianceKwargs" } }, "required": [ "name", "kwargs" ], "title": "model.v0_4.ScaleMeanVarianceDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ScaleMeanVarianceKwargs": { "type": "object", "description": "key word arguments for `ScaleMeanVarianceDescr`", "properties": { "mode": { "description": "Mode for computing mean and variance.\n| mode | description |\n| ----------- | ------------------------------------ |\n| per_dataset | Compute for the entire dataset |\n| per_sample | Compute for each sample individually |", "enum": [ "per_dataset", "per_sample" ], "title": "Mode", "type": "string" }, "reference_tensor": { "description": "Name of tensor to match.", "minLength": 1, "title": "TensorName", "type": "string" }, "axes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "The subset of axes to scale jointly.\nFor example xy to normalize the two image axes for 2d data jointly.\nDefault: scale all non-batch axes jointly.", "examples": [ "xy" ], "title": "Axes" }, "eps": { "default": 1e-6, "description": "Epsilon for numeric stability:\n\"`out = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.", "exclusiveMinimum": 0, "maximum": 0.1, "title": "Eps", "type": "number" } }, "required": [ "mode", "reference_tensor" ], "title": "model.v0_4.ScaleMeanVarianceKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ScaleRangeDescr": { "type": "object", "description": "Scale with percentiles.", "properties": { "name": { "const": "scale_range", "title": "Name", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ScaleRangeKwargs" } }, "required": [ "name", "kwargs" ], "title": "model.v0_4.ScaleRangeDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ScaleRangeKwargs": { "type": "object", "description": "key word arguments for `ScaleRangeDescr`\n\nFor `min_percentile`=0.0 (the default) and `max_percentile`=100 (the default)\nthis processing step normalizes data to the [0, 1] intervall.\nFor other percentiles the normalized values will partially be outside the [0, 1]\nintervall. Use `ScaleRange` followed by `ClipDescr` if you want to limit the\nnormalized values to a range.", "properties": { "mode": { "description": "Mode for computing percentiles.\n| mode | description |\n| ----------- | ------------------------------------ |\n| per_dataset | compute for the entire dataset |\n| per_sample | compute for each sample individually |", "enum": [ "per_dataset", "per_sample" ], "title": "Mode", "type": "string" }, "axes": { "description": "The subset of axes to normalize jointly.\nFor example xy to normalize the two image axes for 2d data jointly.", "examples": [ "xy" ], "title": "Axes", "type": "string" }, "min_percentile": { "anyOf": [ { "type": "integer" }, { "type": "number" } ], "default": 0.0, "description": "The lower percentile used to determine the value to align with zero.", "ge": 0, "lt": 100, "title": "Min Percentile" }, "max_percentile": { "anyOf": [ { "type": "integer" }, { "type": "number" } ], "default": 100.0, "description": "The upper percentile used to determine the value to align with one.\nHas to be bigger than `min_percentile`.\nThe range is 1 to 100 instead of 0 to 100 to avoid mistakenly\naccepting percentiles specified in the range 0.0 to 1.0.", "gt": 1, "le": 100, "title": "Max Percentile" }, "eps": { "default": 1e-6, "description": "Epsilon for numeric stability.\n`out = (tensor - v_lower) / (v_upper - v_lower + eps)`;\nwith `v_lower,v_upper` values at the respective percentiles.", "exclusiveMinimum": 0, "maximum": 0.1, "title": "Eps", "type": "number" }, "reference_tensor": { "anyOf": [ { "minLength": 1, "title": "TensorName", "type": "string" }, { "type": "null" } ], "default": null, "description": "Tensor name to compute the percentiles from. Default: The tensor itself.\nFor any tensor in `inputs` only input tensor references are allowed.\nFor a tensor in `outputs` only input tensor refereences are allowed if `mode: per_dataset`", "title": "Reference Tensor" } }, "required": [ "mode", "axes" ], "title": "model.v0_4.ScaleRangeKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_4__SigmoidDescr": { "type": "object", "description": "The logistic sigmoid funciton, a.k.a. expit function.", "properties": { "name": { "const": "sigmoid", "title": "Name", "type": "string" } }, "required": [ "name" ], "title": "model.v0_4.SigmoidDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__TensorflowJsWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The multi-file weights.\nAll required files/folders should be a zip archive.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "Attachments that are specific to this weights entry." }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "dependencies": { "anyOf": [ { "pattern": "^.+:.+$", "title": "Dependencies", "type": "string" }, { "type": "null" } ], "default": null, "description": "Dependency manager and dependency file, specified as `:`.", "examples": [ "conda:environment.yaml", "maven:./pom.xml", "pip:./requirements.txt" ], "title": "Dependencies" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "tensorflow_version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "Version of the TensorFlow library used." } }, "required": [ "source" ], "title": "model.v0_4.TensorflowJsWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__TensorflowSavedModelBundleWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "Attachments that are specific to this weights entry." }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "dependencies": { "anyOf": [ { "pattern": "^.+:.+$", "title": "Dependencies", "type": "string" }, { "type": "null" } ], "default": null, "description": "Dependency manager and dependency file, specified as `:`.", "examples": [ "conda:environment.yaml", "maven:./pom.xml", "pip:./requirements.txt" ], "title": "Dependencies" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "tensorflow_version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "Version of the TensorFlow library used." } }, "required": [ "source" ], "title": "model.v0_4.TensorflowSavedModelBundleWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__TorchscriptWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "Attachments that are specific to this weights entry." }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "dependencies": { "anyOf": [ { "pattern": "^.+:.+$", "title": "Dependencies", "type": "string" }, { "type": "null" } ], "default": null, "description": "Dependency manager and dependency file, specified as `:`.", "examples": [ "conda:environment.yaml", "maven:./pom.xml", "pip:./requirements.txt" ], "title": "Dependencies" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "pytorch_version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "Version of the PyTorch library used." } }, "required": [ "source" ], "title": "model.v0_4.TorchscriptWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__WeightsDescr": { "type": "object", "properties": { "keras_hdf5": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__KerasHdf5WeightsDescr" }, { "type": "null" } ], "default": null }, "onnx": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__OnnxWeightsDescr" }, { "type": "null" } ], "default": null }, "pytorch_state_dict": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__PytorchStateDictWeightsDescr" }, { "type": "null" } ], "default": null }, "tensorflow_js": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__TensorflowJsWeightsDescr" }, { "type": "null" } ], "default": null }, "tensorflow_saved_model_bundle": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__TensorflowSavedModelBundleWeightsDescr" }, { "type": "null" } ], "default": null }, "torchscript": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__TorchscriptWeightsDescr" }, { "type": "null" } ], "default": null } }, "title": "model.v0_4.WeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceDescr": { "type": "object", "description": "Subtract mean and divide by variance.", "properties": { "name": { "const": "zero_mean_unit_variance", "title": "Name", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceKwargs" } }, "required": [ "name", "kwargs" ], "title": "model.v0_4.ZeroMeanUnitVarianceDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_4__ZeroMeanUnitVarianceKwargs": { "type": "object", "description": "key word arguments for `ZeroMeanUnitVarianceDescr`", "properties": { "mode": { "default": "fixed", "description": "Mode for computing mean and variance.\n| mode | description |\n| ----------- | ------------------------------------ |\n| fixed | Fixed values for mean and variance |\n| per_dataset | Compute for the entire dataset |\n| per_sample | Compute for each sample individually |", "enum": [ "fixed", "per_dataset", "per_sample" ], "title": "Mode", "type": "string" }, "axes": { "description": "The subset of axes to normalize jointly.\nFor example `xy` to normalize the two image axes for 2d data jointly.", "examples": [ "xy" ], "title": "Axes", "type": "string" }, "mean": { "anyOf": [ { "type": "number" }, { "items": { "type": "number" }, "minItems": 1, "type": "array" }, { "type": "null" } ], "default": null, "description": "The mean value(s) to use for `mode: fixed`.\nFor example `[1.1, 2.2, 3.3]` in the case of a 3 channel image with `axes: xy`.", "examples": [ [ 1.1, 2.2, 3.3 ] ], "title": "Mean" }, "std": { "anyOf": [ { "type": "number" }, { "items": { "type": "number" }, "minItems": 1, "type": "array" }, { "type": "null" } ], "default": null, "description": "The standard deviation values to use for `mode: fixed`. Analogous to mean.", "examples": [ [ 0.1, 0.2, 0.3 ] ], "title": "Std" }, "eps": { "default": 1e-6, "description": "epsilon for numeric stability: `out = (tensor - mean) / (std + eps)`.", "exclusiveMinimum": 0, "maximum": 0.1, "title": "Eps", "type": "number" } }, "required": [ "axes" ], "title": "model.v0_4.ZeroMeanUnitVarianceKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_5__BinarizeDescr": { "type": "object", "description": "Binarize the tensor with a fixed threshold.\n\nValues above `BinarizeKwargs.threshold`/`BinarizeAlongAxisKwargs.threshold`\nwill be set to one, values below the threshold to zero.\n\nExamples:\n- in YAML\n ```yaml\n postprocessing:\n - id: binarize\n kwargs:\n axis: 'channel'\n threshold: [0.25, 0.5, 0.75]\n ```\n- in Python:\n\n >>> postprocessing = [BinarizeDescr(\n ... kwargs=BinarizeAlongAxisKwargs(\n ... axis=AxisId('channel'),\n ... threshold=[0.25, 0.5, 0.75],\n ... )\n ... )]", "properties": { "id": { "const": "binarize", "title": "Id", "type": "string" }, "kwargs": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__BinarizeKwargs" }, { "$ref": "#/$defs/BinarizeAlongAxisKwargs" } ], "title": "Kwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.BinarizeDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__BinarizeKwargs": { "type": "object", "description": "key word arguments for `BinarizeDescr`", "properties": { "threshold": { "description": "The fixed threshold", "title": "Threshold", "type": "number" } }, "required": [ "threshold" ], "title": "model.v0_5.BinarizeKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_5__BioimageioConfig": { "type": "object", "properties": { "reproducibility_tolerance": { "default": [], "description": "Tolerances to allow when reproducing the model's test outputs\nfrom the model's test inputs.\nOnly the first entry matching tensor id and weights format is considered.", "items": { "$ref": "#/$defs/ReproducibilityTolerance" }, "title": "Reproducibility Tolerance", "type": "array" }, "funded_by": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Funding agency, grant number if applicable", "title": "Funded By" }, "architecture_type": { "anyOf": [ { "maxLength": 32, "type": "string" }, { "type": "null" } ], "default": null, "description": "Model architecture type, e.g., 3D U-Net, ResNet, transformer", "title": "Architecture Type" }, "architecture_description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Text description of model architecture.", "title": "Architecture Description" }, "modality": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Input modality, e.g., fluorescence microscopy, electron microscopy", "title": "Modality" }, "target_structure": { "description": "Biological structure(s) the model is designed to analyze, e.g., nuclei, mitochondria, cells", "items": { "type": "string" }, "title": "Target Structure", "type": "array" }, "task": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Bioimage-specific task type, e.g., segmentation, classification, detection, denoising", "title": "Task" }, "new_version": { "anyOf": [ { "minLength": 1, "title": "ModelId", "type": "string" }, { "type": "null" } ], "default": null, "description": "A new version of this model exists with a different model id.", "title": "New Version" }, "out_of_scope_use": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Describe how the model may be misused in bioimage analysis contexts and what users should **not** do with the model.", "title": "Out Of Scope Use" }, "bias_risks_limitations": { "$ref": "#/$defs/BiasRisksLimitations", "description": "Description of known bias, risks, and technical limitations for in-scope model use." }, "model_parameter_count": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "Total number of model parameters.", "title": "Model Parameter Count" }, "training": { "$ref": "#/$defs/TrainingDetails", "description": "Details on how the model was trained." }, "inference_time": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Average inference time per image/tile. Specify hardware and image size. Multiple examples can be given.", "title": "Inference Time" }, "memory_requirements_inference": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "GPU memory needed for inference. Multiple examples with different image size can be given.", "title": "Memory Requirements Inference" }, "memory_requirements_training": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "GPU memory needed for training. Multiple examples with different image/batch sizes can be given.", "title": "Memory Requirements Training" }, "evaluations": { "description": "Quantitative model evaluations.\n\nNote:\n At the moment we recommend to include only a single test dataset\n (with evaluation factors that may mark subsets of the dataset)\n to avoid confusion and make the presentation of results cleaner.", "items": { "$ref": "#/$defs/Evaluation" }, "title": "Evaluations", "type": "array" }, "environmental_impact": { "$ref": "#/$defs/EnvironmentalImpact", "description": "Environmental considerations for model training and deployment" } }, "title": "model.v0_5.BioimageioConfig", "additionalProperties": true }, "bioimageio__spec__model__v0_5__ClipDescr": { "type": "object", "description": "Set tensor values below min to min and above max to max.\n\nSee `ScaleRangeDescr` for examples.", "properties": { "id": { "const": "clip", "title": "Id", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ClipKwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.ClipDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ClipKwargs": { "type": "object", "description": "key word arguments for `ClipDescr`", "properties": { "min": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Minimum value for clipping.\n\nExclusive with `min_percentile`", "title": "Min" }, "min_percentile": { "anyOf": [ { "exclusiveMaximum": 100, "minimum": 0, "type": "number" }, { "type": "null" } ], "default": null, "description": "Minimum percentile for clipping.\n\nExclusive with `min`.\n\nIn range [0, 100).", "title": "Min Percentile" }, "max": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Maximum value for clipping.\n\nExclusive with `max_percentile`.", "title": "Max" }, "max_percentile": { "anyOf": [ { "exclusiveMinimum": 1, "maximum": 100, "type": "number" }, { "type": "null" } ], "default": null, "description": "Maximum percentile for clipping.\n\nExclusive with `max`.\n\nIn range (1, 100].", "title": "Max Percentile" }, "axes": { "anyOf": [ { "items": { "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The subset of axes to determine percentiles jointly,\n\ni.e. axes to reduce to compute min/max from `min_percentile`/`max_percentile`.\nFor example to clip 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape with clipped values per channel, specify `axes=('batch', 'x', 'y')`.\nTo clip samples independently, leave out the 'batch' axis.\n\nOnly valid if `min_percentile` and/or `max_percentile` are set.\n\nDefault: Compute percentiles over all axes jointly.", "examples": [ [ "batch", "x", "y" ] ], "title": "Axes" } }, "title": "model.v0_5.ClipKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_5__Config": { "type": "object", "properties": { "bioimageio": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__BioimageioConfig" }, "stardist": { "$ref": "#/$defs/YamlValue", "default": null } }, "title": "model.v0_5.Config", "additionalProperties": true }, "bioimageio__spec__model__v0_5__InputTensorDescr": { "type": "object", "properties": { "id": { "default": "input", "description": "Input tensor id.\nNo duplicates are allowed across all inputs and outputs.", "maxLength": 32, "minLength": 1, "title": "TensorId", "type": "string" }, "description": { "default": "", "description": "free text description", "maxLength": 128, "title": "Description", "type": "string" }, "axes": { "description": "tensor axes", "items": { "discriminator": { "mapping": { "batch": "#/$defs/BatchAxis", "channel": "#/$defs/ChannelAxis", "index": "#/$defs/IndexInputAxis", "space": "#/$defs/SpaceInputAxis", "time": "#/$defs/TimeInputAxis" }, "propertyName": "type" }, "oneOf": [ { "$ref": "#/$defs/BatchAxis" }, { "$ref": "#/$defs/ChannelAxis" }, { "$ref": "#/$defs/IndexInputAxis" }, { "$ref": "#/$defs/TimeInputAxis" }, { "$ref": "#/$defs/SpaceInputAxis" } ] }, "minItems": 1, "title": "Axes", "type": "array" }, "test_tensor": { "anyOf": [ { "$ref": "#/$defs/FileDescr" }, { "type": "null" } ], "default": null, "description": "An example tensor to use for testing.\nUsing the model with the test input tensors is expected to yield the test output tensors.\nEach test tensor has be a an ndarray in the\n[numpy.lib file format](https://numpy.org/doc/stable/reference/generated/numpy.lib.format.html#module-numpy.lib.format).\nThe file extension must be '.npy'." }, "sample_tensor": { "anyOf": [ { "$ref": "#/$defs/FileDescr" }, { "type": "null" } ], "default": null, "description": "A sample tensor to illustrate a possible input/output for the model,\nThe sample image primarily serves to inform a human user about an example use case\nand is typically stored as .hdf5, .png or .tiff.\nIt has to be readable by the [imageio library](https://imageio.readthedocs.io/en/stable/formats/index.html#supported-formats)\n(numpy's `.npy` format is not supported).\nThe image dimensionality has to match the number of axes specified in this tensor description." }, "data": { "anyOf": [ { "$ref": "#/$defs/NominalOrOrdinalDataDescr" }, { "$ref": "#/$defs/IntervalOrRatioDataDescr" }, { "items": { "anyOf": [ { "$ref": "#/$defs/NominalOrOrdinalDataDescr" }, { "$ref": "#/$defs/IntervalOrRatioDataDescr" } ] }, "minItems": 1, "type": "array" } ], "default": { "type": "float32", "range": [ null, null ], "unit": "arbitrary unit", "scale": 1.0, "offset": null }, "description": "Description of the tensor's data values, optionally per channel.\nIf specified per channel, the data `type` needs to match across channels.", "title": "Data" }, "optional": { "default": false, "description": "indicates that this tensor may be `None`", "title": "Optional", "type": "boolean" }, "preprocessing": { "description": "Description of how this input should be preprocessed.\n\nnotes:\n- If preprocessing does not start with an 'ensure_dtype' entry, it is added\n to ensure an input tensor's data type matches the input tensor's data description.\n- If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, an\n 'ensure_dtype' step is added to ensure preprocessing steps are not unintentionally\n changing the data type.", "items": { "discriminator": { "mapping": { "binarize": "#/$defs/bioimageio__spec__model__v0_5__BinarizeDescr", "clip": "#/$defs/bioimageio__spec__model__v0_5__ClipDescr", "ensure_dtype": "#/$defs/EnsureDtypeDescr", "fixed_zero_mean_unit_variance": "#/$defs/FixedZeroMeanUnitVarianceDescr", "scale_linear": "#/$defs/bioimageio__spec__model__v0_5__ScaleLinearDescr", "scale_range": "#/$defs/bioimageio__spec__model__v0_5__ScaleRangeDescr", "sigmoid": "#/$defs/bioimageio__spec__model__v0_5__SigmoidDescr", "softmax": "#/$defs/SoftmaxDescr", "zero_mean_unit_variance": "#/$defs/bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceDescr" }, "propertyName": "id" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__BinarizeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ClipDescr" }, { "$ref": "#/$defs/EnsureDtypeDescr" }, { "$ref": "#/$defs/FixedZeroMeanUnitVarianceDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleLinearDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleRangeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__SigmoidDescr" }, { "$ref": "#/$defs/SoftmaxDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceDescr" } ] }, "title": "Preprocessing", "type": "array" } }, "required": [ "axes" ], "title": "model.v0_5.InputTensorDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__KerasHdf5WeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "Source of the weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "tensorflow_version": { "$ref": "#/$defs/Version", "description": "TensorFlow version used to create these weights." } }, "required": [ "source", "tensorflow_version" ], "title": "model.v0_5.KerasHdf5WeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__LinkedModel": { "type": "object", "description": "Reference to a bioimage.io model.", "properties": { "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the linked resource following SemVer 2.0." }, "id": { "description": "A valid model `id` from the bioimage.io collection.", "minLength": 1, "title": "ModelId", "type": "string" } }, "required": [ "id" ], "title": "model.v0_5.LinkedModel", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ModelDescr": { "type": "object", "description": "Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.\nThese fields are typically stored in a YAML file which we call a model resource description file (model RDF).", "properties": { "name": { "description": "A human-readable name of this model.\nIt should be no longer than 64 characters\nand may only contain letter, number, underscore, minus, parentheses and spaces.\nWe recommend to chose a name that refers to the model's task and image modality.", "maxLength": 128, "minLength": 5, "title": "Name", "type": "string" }, "description": { "default": "", "description": "A string containing a brief description.", "maxLength": 1024, "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 2, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of the model RDF and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "title": "Authors", "type": "array" }, "attachments": { "description": "file attachments", "items": { "$ref": "#/$defs/FileDescr" }, "title": "Attachments", "type": "array" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__CiteEntry" }, "title": "Cite", "type": "array" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose)\nto discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "git_repo": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration, e.g. on bioimage.io", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified, `authors` are maintainers and at least some of them has to specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Maintainer" }, "title": "Maintainers", "type": "array" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_comment": { "anyOf": [ { "maxLength": 512, "type": "string" }, { "type": "null" } ], "default": null, "description": "A comment on the version of the resource.", "title": "Version Comment" }, "format_version": { "const": "0.5.9", "description": "Version of the bioimage.io model description specification used.\nWhen creating a new model always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.", "title": "Format Version", "type": "string" }, "type": { "const": "model", "description": "Specialized resource type 'model'", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "ModelId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "documentation": { "anyOf": [ { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ] }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.\nThe documentation should include a '#[#] Validation' (sub)section\nwith details on how to quantitatively validate the model on unseen data.", "title": "Documentation" }, "inputs": { "description": "Describes the input tensors expected by this model.", "items": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__InputTensorDescr" }, "minItems": 1, "title": "Inputs", "type": "array" }, "outputs": { "description": "Describes the output tensors.", "items": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__OutputTensorDescr" }, "minItems": 1, "title": "Outputs", "type": "array" }, "packaged_by": { "description": "The persons that have packaged and uploaded this model.\nOnly required if those persons differ from the `authors`.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "title": "Packaged By", "type": "array" }, "parent": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__LinkedModel" }, { "type": "null" } ], "default": null, "description": "The model from which this model is derived, e.g. by fine-tuning the weights." }, "run_mode": { "anyOf": [ { "$ref": "#/$defs/RunMode" }, { "type": "null" } ], "default": null, "description": "Custom run mode for this model: for more complex prediction procedures like test time\ndata augmentation that currently cannot be expressed in the specification.\nNo standard run modes are defined yet." }, "timestamp": { "$ref": "#/$defs/Datetime", "description": "Timestamp in [ISO 8601](# format\nwith a few restrictions listed [here](https://docs.python.org/3/library/datetime.html#datetime.datetime.fromisoformat).\n(In Python a datetime object is valid, too)." }, "training_data": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__dataset__v0_3__LinkedDataset" }, { "$ref": "#/$defs/bioimageio__spec__dataset__v0_3__DatasetDescr" }, { "$ref": "#/$defs/bioimageio__spec__dataset__v0_2__DatasetDescr" }, { "type": "null" } ], "default": null, "description": "The dataset used to train this model", "title": "Training Data" }, "weights": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__WeightsDescr", "description": "The weights for this model.\nWeights can be given for different formats, but should otherwise be equivalent.\nThe available weight formats determine which consumers can use this model." }, "config": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__Config" } }, "required": [ "name", "format_version", "type", "inputs", "outputs", "weights" ], "title": "model 0.5.9", "additionalProperties": false }, "bioimageio__spec__model__v0_5__OnnxWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "Source of the weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "opset_version": { "description": "ONNX opset version", "minimum": 7, "title": "Opset Version", "type": "integer" }, "external_data": { "anyOf": [ { "$ref": "#/$defs/FileDescr", "examples": [ { "source": "weights.onnx.data" } ] }, { "type": "null" } ], "default": null, "description": "Source of the external ONNX data file holding the weights.\n(If present **source** holds the ONNX architecture without weights)." } }, "required": [ "source", "opset_version" ], "title": "model.v0_5.OnnxWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__OutputTensorDescr": { "type": "object", "properties": { "id": { "default": "output", "description": "Output tensor id.\nNo duplicates are allowed across all inputs and outputs.", "maxLength": 32, "minLength": 1, "title": "TensorId", "type": "string" }, "description": { "default": "", "description": "free text description", "maxLength": 128, "title": "Description", "type": "string" }, "axes": { "description": "tensor axes", "items": { "discriminator": { "mapping": { "batch": "#/$defs/BatchAxis", "channel": "#/$defs/ChannelAxis", "index": "#/$defs/IndexOutputAxis", "space": { "oneOf": [ { "$ref": "#/$defs/SpaceOutputAxis" }, { "$ref": "#/$defs/SpaceOutputAxisWithHalo" } ] }, "time": { "oneOf": [ { "$ref": "#/$defs/TimeOutputAxis" }, { "$ref": "#/$defs/TimeOutputAxisWithHalo" } ] } }, "propertyName": "type" }, "oneOf": [ { "$ref": "#/$defs/BatchAxis" }, { "$ref": "#/$defs/ChannelAxis" }, { "$ref": "#/$defs/IndexOutputAxis" }, { "oneOf": [ { "$ref": "#/$defs/TimeOutputAxis" }, { "$ref": "#/$defs/TimeOutputAxisWithHalo" } ] }, { "oneOf": [ { "$ref": "#/$defs/SpaceOutputAxis" }, { "$ref": "#/$defs/SpaceOutputAxisWithHalo" } ] } ] }, "minItems": 1, "title": "Axes", "type": "array" }, "test_tensor": { "anyOf": [ { "$ref": "#/$defs/FileDescr" }, { "type": "null" } ], "default": null, "description": "An example tensor to use for testing.\nUsing the model with the test input tensors is expected to yield the test output tensors.\nEach test tensor has be a an ndarray in the\n[numpy.lib file format](https://numpy.org/doc/stable/reference/generated/numpy.lib.format.html#module-numpy.lib.format).\nThe file extension must be '.npy'." }, "sample_tensor": { "anyOf": [ { "$ref": "#/$defs/FileDescr" }, { "type": "null" } ], "default": null, "description": "A sample tensor to illustrate a possible input/output for the model,\nThe sample image primarily serves to inform a human user about an example use case\nand is typically stored as .hdf5, .png or .tiff.\nIt has to be readable by the [imageio library](https://imageio.readthedocs.io/en/stable/formats/index.html#supported-formats)\n(numpy's `.npy` format is not supported).\nThe image dimensionality has to match the number of axes specified in this tensor description." }, "data": { "anyOf": [ { "$ref": "#/$defs/NominalOrOrdinalDataDescr" }, { "$ref": "#/$defs/IntervalOrRatioDataDescr" }, { "items": { "anyOf": [ { "$ref": "#/$defs/NominalOrOrdinalDataDescr" }, { "$ref": "#/$defs/IntervalOrRatioDataDescr" } ] }, "minItems": 1, "type": "array" } ], "default": { "type": "float32", "range": [ null, null ], "unit": "arbitrary unit", "scale": 1.0, "offset": null }, "description": "Description of the tensor's data values, optionally per channel.\nIf specified per channel, the data `type` needs to match across channels.", "title": "Data" }, "postprocessing": { "description": "Description of how this output should be postprocessed.\n\nnote: `postprocessing` always ends with an 'ensure_dtype' operation.\n If not given this is added to cast to this tensor's `data.type`.", "items": { "discriminator": { "mapping": { "binarize": "#/$defs/bioimageio__spec__model__v0_5__BinarizeDescr", "clip": "#/$defs/bioimageio__spec__model__v0_5__ClipDescr", "ensure_dtype": "#/$defs/EnsureDtypeDescr", "fixed_zero_mean_unit_variance": "#/$defs/FixedZeroMeanUnitVarianceDescr", "scale_linear": "#/$defs/bioimageio__spec__model__v0_5__ScaleLinearDescr", "scale_mean_variance": "#/$defs/bioimageio__spec__model__v0_5__ScaleMeanVarianceDescr", "scale_range": "#/$defs/bioimageio__spec__model__v0_5__ScaleRangeDescr", "sigmoid": "#/$defs/bioimageio__spec__model__v0_5__SigmoidDescr", "softmax": "#/$defs/SoftmaxDescr", "stardist_postprocessing": "#/$defs/StardistPostprocessingDescr", "zero_mean_unit_variance": "#/$defs/bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceDescr" }, "propertyName": "id" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__BinarizeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ClipDescr" }, { "$ref": "#/$defs/EnsureDtypeDescr" }, { "$ref": "#/$defs/FixedZeroMeanUnitVarianceDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleLinearDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleMeanVarianceDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleRangeDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__SigmoidDescr" }, { "$ref": "#/$defs/SoftmaxDescr" }, { "$ref": "#/$defs/StardistPostprocessingDescr" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceDescr" } ] }, "title": "Postprocessing", "type": "array" } }, "required": [ "axes" ], "title": "model.v0_5.OutputTensorDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__PytorchStateDictWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "Source of the weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "architecture": { "anyOf": [ { "$ref": "#/$defs/ArchitectureFromFileDescr" }, { "$ref": "#/$defs/ArchitectureFromLibraryDescr" } ], "title": "Architecture" }, "pytorch_version": { "$ref": "#/$defs/Version", "description": "Version of the PyTorch library used.\nIf `architecture.depencencies` is specified it has to include pytorch and any version pinning has to be compatible." }, "dependencies": { "anyOf": [ { "$ref": "#/$defs/FileDescr", "examples": [ { "source": "environment.yaml" } ] }, { "type": "null" } ], "default": null, "description": "Custom depencies beyond pytorch described in a Conda environment file.\nAllows to specify custom dependencies, see conda docs:\n- [Exporting an environment file across platforms](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#exporting-an-environment-file-across-platforms)\n- [Creating an environment file manually](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually)\n\nThe conda environment file should include pytorch and any version pinning has to be compatible with\n**pytorch_version**." } }, "required": [ "source", "architecture", "pytorch_version" ], "title": "model.v0_5.PytorchStateDictWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ScaleLinearDescr": { "type": "object", "description": "Fixed linear scaling.\n\nExamples:\n 1. Scale with scalar gain and offset\n - in YAML\n ```yaml\n preprocessing:\n - id: scale_linear\n kwargs:\n gain: 2.0\n offset: 3.0\n ```\n - in Python:\n\n >>> preprocessing = [\n ... ScaleLinearDescr(kwargs=ScaleLinearKwargs(gain= 2.0, offset=3.0))\n ... ]\n\n 2. Independent scaling along an axis\n - in YAML\n ```yaml\n preprocessing:\n - id: scale_linear\n kwargs:\n axis: 'channel'\n gain: [1.0, 2.0, 3.0]\n ```\n - in Python:\n\n >>> preprocessing = [\n ... ScaleLinearDescr(\n ... kwargs=ScaleLinearAlongAxisKwargs(\n ... axis=AxisId(\"channel\"),\n ... gain=[1.0, 2.0, 3.0],\n ... )\n ... )\n ... ]", "properties": { "id": { "const": "scale_linear", "title": "Id", "type": "string" }, "kwargs": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleLinearKwargs" }, { "$ref": "#/$defs/ScaleLinearAlongAxisKwargs" } ], "title": "Kwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.ScaleLinearDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ScaleLinearKwargs": { "type": "object", "description": "Key word arguments for `ScaleLinearDescr`", "properties": { "gain": { "default": 1.0, "description": "multiplicative factor", "title": "Gain", "type": "number" }, "offset": { "default": 0.0, "description": "additive term", "title": "Offset", "type": "number" } }, "title": "model.v0_5.ScaleLinearKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ScaleMeanVarianceDescr": { "type": "object", "description": "Scale a tensor's data distribution to match another tensor's mean/std.\n`out = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.`", "properties": { "id": { "const": "scale_mean_variance", "title": "Id", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleMeanVarianceKwargs" } }, "required": [ "id", "kwargs" ], "title": "model.v0_5.ScaleMeanVarianceDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ScaleMeanVarianceKwargs": { "type": "object", "description": "key word arguments for `ScaleMeanVarianceKwargs`", "properties": { "reference_tensor": { "description": "ID of unprocessed input tensor to match.", "maxLength": 32, "minLength": 1, "title": "TensorId", "type": "string" }, "axes": { "anyOf": [ { "items": { "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The subset of axes to normalize jointly, i.e. axes to reduce to compute mean/std.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify `axes=('batch', 'x', 'y')`.\nTo normalize samples independently, leave out the 'batch' axis.\nDefault: Scale all axes jointly.", "examples": [ [ "batch", "x", "y" ] ], "title": "Axes" }, "eps": { "default": 1e-6, "description": "Epsilon for numeric stability:\n`out = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.`", "exclusiveMinimum": 0, "maximum": 0.1, "title": "Eps", "type": "number" } }, "required": [ "reference_tensor" ], "title": "model.v0_5.ScaleMeanVarianceKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ScaleRangeDescr": { "type": "object", "description": "Scale with percentiles.\n\nExamples:\n1. Scale linearly to map 5th percentile to 0 and 99.8th percentile to 1.0\n - in YAML\n ```yaml\n preprocessing:\n - id: scale_range\n kwargs:\n axes: ['y', 'x']\n max_percentile: 99.8\n min_percentile: 5.0\n ```\n - in Python\n\n >>> preprocessing = [\n ... ScaleRangeDescr(\n ... kwargs=ScaleRangeKwargs(\n ... axes= (AxisId('y'), AxisId('x')),\n ... max_percentile= 99.8,\n ... min_percentile= 5.0,\n ... )\n ... )\n ... ]\n\n 2. Combine the above scaling with additional clipping to clip values outside the range given by the percentiles.\n - in YAML\n ```yaml\n preprocessing:\n - id: scale_range\n kwargs:\n axes: ['y', 'x']\n max_percentile: 99.8\n min_percentile: 5.0\n - id: clip\n kwargs:\n min: 0.0\n max: 1.0\n ```\n - in Python\n\n >>> preprocessing = [\n ... ScaleRangeDescr(\n ... kwargs=ScaleRangeKwargs(\n ... axes= (AxisId('y'), AxisId('x')),\n ... max_percentile= 99.8,\n ... min_percentile= 5.0,\n ... )\n ... ),\n ... ClipDescr(\n ... kwargs=ClipKwargs(\n ... min=0.0,\n ... max=1.0,\n ... )\n ... ),\n ... ]", "properties": { "id": { "const": "scale_range", "title": "Id", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ScaleRangeKwargs" } }, "required": [ "id" ], "title": "model.v0_5.ScaleRangeDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ScaleRangeKwargs": { "type": "object", "description": "key word arguments for `ScaleRangeDescr`\n\nFor `min_percentile`=0.0 (the default) and `max_percentile`=100 (the default)\nthis processing step normalizes data to the [0, 1] intervall.\nFor other percentiles the normalized values will partially be outside the [0, 1]\nintervall. Use `ScaleRange` followed by `ClipDescr` if you want to limit the\nnormalized values to a range.", "properties": { "axes": { "anyOf": [ { "items": { "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The subset of axes to normalize jointly, i.e. axes to reduce to compute the min/max percentile value.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify `axes=('batch', 'x', 'y')`.\nTo normalize samples independently, leave out the \"batch\" axis.\nDefault: Scale all axes jointly.", "examples": [ [ "batch", "x", "y" ] ], "title": "Axes" }, "min_percentile": { "default": 0.0, "description": "The lower percentile used to determine the value to align with zero.", "exclusiveMaximum": 100, "minimum": 0, "title": "Min Percentile", "type": "number" }, "max_percentile": { "default": 100.0, "description": "The upper percentile used to determine the value to align with one.\nHas to be bigger than `min_percentile`.\nThe range is 1 to 100 instead of 0 to 100 to avoid mistakenly\naccepting percentiles specified in the range 0.0 to 1.0.", "exclusiveMinimum": 1, "maximum": 100, "title": "Max Percentile", "type": "number" }, "eps": { "default": 1e-6, "description": "Epsilon for numeric stability.\n`out = (tensor - v_lower) / (v_upper - v_lower + eps)`;\nwith `v_lower,v_upper` values at the respective percentiles.", "exclusiveMinimum": 0, "maximum": 0.1, "title": "Eps", "type": "number" }, "reference_tensor": { "anyOf": [ { "maxLength": 32, "minLength": 1, "title": "TensorId", "type": "string" }, { "type": "null" } ], "default": null, "description": "ID of the unprocessed input tensor to compute the percentiles from.\nDefault: The tensor itself.", "title": "Reference Tensor" } }, "title": "model.v0_5.ScaleRangeKwargs", "additionalProperties": false }, "bioimageio__spec__model__v0_5__SigmoidDescr": { "type": "object", "description": "The logistic sigmoid function, a.k.a. expit function.\n\nExamples:\n- in YAML\n ```yaml\n postprocessing:\n - id: sigmoid\n ```\n- in Python:\n\n >>> postprocessing = [SigmoidDescr()]", "properties": { "id": { "const": "sigmoid", "title": "Id", "type": "string" } }, "required": [ "id" ], "title": "model.v0_5.SigmoidDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__TensorflowJsWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The multi-file weights.\nAll required files/folders should be a zip archive.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "tensorflow_version": { "$ref": "#/$defs/Version", "description": "Version of the TensorFlow library used." } }, "required": [ "source", "tensorflow_version" ], "title": "model.v0_5.TensorflowJsWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__TensorflowSavedModelBundleWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "The multi-file weights.\nAll required files/folders should be a zip archive.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "tensorflow_version": { "$ref": "#/$defs/Version", "description": "Version of the TensorFlow library used." }, "dependencies": { "anyOf": [ { "$ref": "#/$defs/FileDescr", "examples": [ { "source": "environment.yaml" } ] }, { "type": "null" } ], "default": null, "description": "Custom dependencies beyond tensorflow.\nShould include tensorflow and any version pinning has to be compatible with **tensorflow_version**." } }, "required": [ "source", "tensorflow_version" ], "title": "model.v0_5.TensorflowSavedModelBundleWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__TorchscriptWeightsDescr": { "type": "object", "properties": { "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "description": "Source of the weights file.", "title": "Source" }, "sha256": { "anyOf": [ { "description": "A SHA-256 hash value", "maxLength": 64, "minLength": 64, "title": "Sha256", "type": "string" }, { "type": "null" } ], "default": null, "description": "SHA256 hash value of the **source** file.", "title": "Sha256" }, "authors": { "anyOf": [ { "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "Authors\nEither the person(s) that have trained this model resulting in the original weights file.\n (If this is the initial weights entry, i.e. it does not have a `parent`)\nOr the person(s) who have converted the weights to this weights format.\n (If this is a child weight, i.e. it has a `parent` field)", "title": "Authors" }, "parent": { "anyOf": [ { "enum": [ "keras_hdf5", "keras_v3", "onnx", "pytorch_state_dict", "tensorflow_js", "tensorflow_saved_model_bundle", "torchscript" ], "type": "string" }, { "type": "null" } ], "default": null, "description": "The source weights these weights were converted from.\nFor example, if a model's weights were converted from the `pytorch_state_dict` format to `torchscript`,\nThe `pytorch_state_dict` weights entry has no `parent` and is the parent of the `torchscript` weights.\nAll weight entries except one (the initial set of weights resulting from training the model),\nneed to have this field.", "examples": [ "pytorch_state_dict" ], "title": "Parent" }, "comment": { "default": "", "description": "A comment about this weights entry, for example how these weights were created.", "title": "Comment", "type": "string" }, "pytorch_version": { "$ref": "#/$defs/Version", "description": "Version of the PyTorch library used." } }, "required": [ "source", "pytorch_version" ], "title": "model.v0_5.TorchscriptWeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__WeightsDescr": { "type": "object", "properties": { "keras_hdf5": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__KerasHdf5WeightsDescr" }, { "type": "null" } ], "default": null }, "keras_v3": { "anyOf": [ { "$ref": "#/$defs/KerasV3WeightsDescr" }, { "type": "null" } ], "default": null }, "onnx": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__OnnxWeightsDescr" }, { "type": "null" } ], "default": null }, "pytorch_state_dict": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__PytorchStateDictWeightsDescr" }, { "type": "null" } ], "default": null }, "tensorflow_js": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__TensorflowJsWeightsDescr" }, { "type": "null" } ], "default": null }, "tensorflow_saved_model_bundle": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__TensorflowSavedModelBundleWeightsDescr" }, { "type": "null" } ], "default": null }, "torchscript": { "anyOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_5__TorchscriptWeightsDescr" }, { "type": "null" } ], "default": null } }, "title": "model.v0_5.WeightsDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceDescr": { "type": "object", "description": "Subtract mean and divide by variance.\n\nExamples:\n Subtract tensor mean and variance\n - in YAML\n ```yaml\n preprocessing:\n - id: zero_mean_unit_variance\n ```\n - in Python\n >>> preprocessing = [ZeroMeanUnitVarianceDescr()]", "properties": { "id": { "const": "zero_mean_unit_variance", "title": "Id", "type": "string" }, "kwargs": { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceKwargs" } }, "required": [ "id" ], "title": "model.v0_5.ZeroMeanUnitVarianceDescr", "additionalProperties": false }, "bioimageio__spec__model__v0_5__ZeroMeanUnitVarianceKwargs": { "type": "object", "description": "key word arguments for `ZeroMeanUnitVarianceDescr`", "properties": { "axes": { "anyOf": [ { "items": { "maxLength": 16, "minLength": 1, "title": "AxisId", "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "description": "The subset of axes to normalize jointly, i.e. axes to reduce to compute mean/std.\nFor example to normalize 'batch', 'x' and 'y' jointly in a tensor ('batch', 'channel', 'y', 'x')\nresulting in a tensor of equal shape normalized per channel, specify `axes=('batch', 'x', 'y')`.\nTo normalize each sample independently leave out the 'batch' axis.\nDefault: Scale all axes jointly.", "examples": [ [ "batch", "x", "y" ] ], "title": "Axes" }, "eps": { "default": 1e-6, "description": "epsilon for numeric stability: `out = (tensor - mean) / (std + eps)`.", "exclusiveMinimum": 0, "maximum": 0.1, "title": "Eps", "type": "number" } }, "title": "model.v0_5.ZeroMeanUnitVarianceKwargs", "additionalProperties": false }, "bioimageio__spec__notebook__v0_2__NotebookDescr": { "type": "object", "description": "Bioimage.io description of a Jupyter Notebook.", "properties": { "name": { "description": "A human-friendly name of the resource description", "minLength": 1, "title": "Name", "type": "string" }, "description": { "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 1, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of the RDF and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Author" }, "title": "Authors", "type": "array" }, "attachments": { "anyOf": [ { "$ref": "#/$defs/AttachmentsDescr" }, { "type": "null" } ], "default": null, "description": "file and other attachments" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__CiteEntry" }, "title": "Cite", "type": "array" }, "config": { "type": "object", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a github repo URL in `config` since we already have the\n`git_repo` field defined in the spec.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n bioimageio: # here is the domain name\n my_custom_key: 3837283\n another_key:\n nested: value\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource\n(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files)", "examples": [ { "bioimageio": { "another_key": { "nested": "value" }, "my_custom_key": 3837283 }, "imagej": { "macro_dir": "path/to/macro/file" } } ], "title": "Config", "additionalProperties": { "$ref": "#/$defs/YamlValue" } }, "download_url": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL to download the resource from (deprecated)", "title": "Download Url" }, "git_repo": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified `authors` are maintainers and at least some of them should specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_2__Maintainer" }, "title": "Maintainers", "type": "array" }, "rdf_source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.\nDo not set this field in a YAML file.", "title": "Rdf Source" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_number": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "description": "version number (n-th published version, not the semantic version)", "title": "Version Number" }, "format_version": { "const": "0.2.4", "description": "The format version of this resource specification\n(not the `version` of the resource description)\nWhen creating a new resource always use the latest micro/patch version described here.\nThe `format_version` is important for any consumer software to understand how to parse the fields.", "title": "Format Version", "type": "string" }, "badges": { "description": "badges associated with this resource", "items": { "$ref": "#/$defs/BadgeDescr" }, "title": "Badges", "type": "array" }, "documentation": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.", "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ], "title": "Documentation" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose\n) to discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "type": { "const": "notebook", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "NotebookId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" } ], "description": "The Jupyter notebook", "title": "Source" } }, "required": [ "name", "description", "format_version", "type", "source" ], "title": "notebook 0.2.4", "additionalProperties": false }, "bioimageio__spec__notebook__v0_3__NotebookDescr": { "type": "object", "description": "Bioimage.io description of a Jupyter notebook.", "properties": { "name": { "description": "A human-friendly name of the resource description.\nMay only contains letters, digits, underscore, minus, parentheses and spaces.", "maxLength": 128, "minLength": 5, "title": "Name", "type": "string" }, "description": { "default": "", "description": "A string containing a brief description.", "maxLength": 1024, "title": "Description", "type": "string" }, "covers": { "description": "Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.\nThe supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')", "examples": [ [ "cover.png" ] ], "items": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ] }, "title": "Covers", "type": "array" }, "id_emoji": { "anyOf": [ { "examples": [ "🦈", "🦥" ], "maxLength": 2, "minLength": 1, "type": "string" }, { "type": "null" } ], "default": null, "description": "UTF-8 emoji for display alongside the `id`.", "title": "Id Emoji" }, "authors": { "description": "The authors are the creators of this resource description and the primary points of contact.", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Author" }, "title": "Authors", "type": "array" }, "attachments": { "description": "file attachments", "items": { "$ref": "#/$defs/FileDescr" }, "title": "Attachments", "type": "array" }, "cite": { "description": "citations", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__CiteEntry" }, "title": "Cite", "type": "array" }, "license": { "anyOf": [ { "enum": [ "0BSD", "3D-Slicer-1.0", "AAL", "Abstyles", "AdaCore-doc", "Adobe-2006", "Adobe-Display-PostScript", "Adobe-Glyph", "Adobe-Utopia", "ADSL", "AFL-1.1", "AFL-1.2", "AFL-2.0", "AFL-2.1", "AFL-3.0", "Afmparse", "AGPL-1.0-only", "AGPL-1.0-or-later", "AGPL-3.0-only", "AGPL-3.0-or-later", "Aladdin", "AMD-newlib", "AMDPLPA", "AML", "AML-glslang", "AMPAS", "ANTLR-PD", "ANTLR-PD-fallback", "any-OSI", "any-OSI-perl-modules", "Apache-1.0", "Apache-1.1", "Apache-2.0", "APAFML", "APL-1.0", "App-s2p", "APSL-1.0", "APSL-1.1", "APSL-1.2", "APSL-2.0", "Arphic-1999", "Artistic-1.0", "Artistic-1.0-cl8", "Artistic-1.0-Perl", "Artistic-2.0", "Artistic-dist", "Aspell-RU", "ASWF-Digital-Assets-1.0", "ASWF-Digital-Assets-1.1", "Baekmuk", "Bahyph", "Barr", "bcrypt-Solar-Designer", "Beerware", "Bitstream-Charter", "Bitstream-Vera", "BitTorrent-1.0", "BitTorrent-1.1", "blessing", "BlueOak-1.0.0", "Boehm-GC", "Boehm-GC-without-fee", "Borceux", "Brian-Gladman-2-Clause", "Brian-Gladman-3-Clause", "BSD-1-Clause", "BSD-2-Clause", "BSD-2-Clause-Darwin", "BSD-2-Clause-first-lines", "BSD-2-Clause-Patent", "BSD-2-Clause-pkgconf-disclaimer", "BSD-2-Clause-Views", "BSD-3-Clause", "BSD-3-Clause-acpica", "BSD-3-Clause-Attribution", "BSD-3-Clause-Clear", "BSD-3-Clause-flex", "BSD-3-Clause-HP", "BSD-3-Clause-LBNL", "BSD-3-Clause-Modification", "BSD-3-Clause-No-Military-License", "BSD-3-Clause-No-Nuclear-License", "BSD-3-Clause-No-Nuclear-License-2014", "BSD-3-Clause-No-Nuclear-Warranty", "BSD-3-Clause-Open-MPI", "BSD-3-Clause-Sun", "BSD-4-Clause", "BSD-4-Clause-Shortened", "BSD-4-Clause-UC", "BSD-4.3RENO", "BSD-4.3TAHOE", "BSD-Advertising-Acknowledgement", "BSD-Attribution-HPND-disclaimer", "BSD-Inferno-Nettverk", "BSD-Protection", "BSD-Source-beginning-file", "BSD-Source-Code", "BSD-Systemics", "BSD-Systemics-W3Works", "BSL-1.0", "BUSL-1.1", "bzip2-1.0.6", "C-UDA-1.0", "CAL-1.0", "CAL-1.0-Combined-Work-Exception", "Caldera", "Caldera-no-preamble", "Catharon", "CATOSL-1.1", "CC-BY-1.0", "CC-BY-2.0", "CC-BY-2.5", "CC-BY-2.5-AU", "CC-BY-3.0", "CC-BY-3.0-AT", "CC-BY-3.0-AU", "CC-BY-3.0-DE", "CC-BY-3.0-IGO", "CC-BY-3.0-NL", "CC-BY-3.0-US", "CC-BY-4.0", "CC-BY-NC-1.0", "CC-BY-NC-2.0", "CC-BY-NC-2.5", "CC-BY-NC-3.0", "CC-BY-NC-3.0-DE", "CC-BY-NC-4.0", "CC-BY-NC-ND-1.0", "CC-BY-NC-ND-2.0", "CC-BY-NC-ND-2.5", "CC-BY-NC-ND-3.0", "CC-BY-NC-ND-3.0-DE", "CC-BY-NC-ND-3.0-IGO", "CC-BY-NC-ND-4.0", "CC-BY-NC-SA-1.0", "CC-BY-NC-SA-2.0", "CC-BY-NC-SA-2.0-DE", "CC-BY-NC-SA-2.0-FR", "CC-BY-NC-SA-2.0-UK", "CC-BY-NC-SA-2.5", "CC-BY-NC-SA-3.0", "CC-BY-NC-SA-3.0-DE", "CC-BY-NC-SA-3.0-IGO", "CC-BY-NC-SA-4.0", "CC-BY-ND-1.0", "CC-BY-ND-2.0", "CC-BY-ND-2.5", "CC-BY-ND-3.0", "CC-BY-ND-3.0-DE", "CC-BY-ND-4.0", "CC-BY-SA-1.0", "CC-BY-SA-2.0", "CC-BY-SA-2.0-UK", "CC-BY-SA-2.1-JP", "CC-BY-SA-2.5", "CC-BY-SA-3.0", "CC-BY-SA-3.0-AT", "CC-BY-SA-3.0-DE", "CC-BY-SA-3.0-IGO", "CC-BY-SA-4.0", "CC-PDDC", "CC-PDM-1.0", "CC-SA-1.0", "CC0-1.0", "CDDL-1.0", "CDDL-1.1", "CDL-1.0", "CDLA-Permissive-1.0", "CDLA-Permissive-2.0", "CDLA-Sharing-1.0", "CECILL-1.0", "CECILL-1.1", "CECILL-2.0", "CECILL-2.1", "CECILL-B", "CECILL-C", "CERN-OHL-1.1", "CERN-OHL-1.2", "CERN-OHL-P-2.0", "CERN-OHL-S-2.0", "CERN-OHL-W-2.0", "CFITSIO", "check-cvs", "checkmk", "ClArtistic", "Clips", "CMU-Mach", "CMU-Mach-nodoc", "CNRI-Jython", "CNRI-Python", "CNRI-Python-GPL-Compatible", "COIL-1.0", "Community-Spec-1.0", "Condor-1.1", "copyleft-next-0.3.0", "copyleft-next-0.3.1", "Cornell-Lossless-JPEG", "CPAL-1.0", "CPL-1.0", "CPOL-1.02", "Cronyx", "Crossword", "CryptoSwift", "CrystalStacker", "CUA-OPL-1.0", "Cube", "curl", "cve-tou", "D-FSL-1.0", "DEC-3-Clause", "diffmark", "DL-DE-BY-2.0", "DL-DE-ZERO-2.0", "DOC", "DocBook-DTD", "DocBook-Schema", "DocBook-Stylesheet", "DocBook-XML", "Dotseqn", "DRL-1.0", "DRL-1.1", "DSDP", "dtoa", "dvipdfm", "ECL-1.0", "ECL-2.0", "EFL-1.0", "EFL-2.0", "eGenix", "Elastic-2.0", "Entessa", "EPICS", "EPL-1.0", "EPL-2.0", "ErlPL-1.1", "etalab-2.0", "EUDatagrid", "EUPL-1.0", "EUPL-1.1", "EUPL-1.2", "Eurosym", "Fair", "FBM", "FDK-AAC", "Ferguson-Twofish", "Frameworx-1.0", "FreeBSD-DOC", "FreeImage", "FSFAP", "FSFAP-no-warranty-disclaimer", "FSFUL", "FSFULLR", "FSFULLRSD", "FSFULLRWD", "FSL-1.1-ALv2", "FSL-1.1-MIT", "FTL", "Furuseth", "fwlw", "Game-Programming-Gems", "GCR-docs", "GD", "generic-xts", "GFDL-1.1-invariants-only", "GFDL-1.1-invariants-or-later", "GFDL-1.1-no-invariants-only", "GFDL-1.1-no-invariants-or-later", "GFDL-1.1-only", "GFDL-1.1-or-later", "GFDL-1.2-invariants-only", "GFDL-1.2-invariants-or-later", "GFDL-1.2-no-invariants-only", "GFDL-1.2-no-invariants-or-later", "GFDL-1.2-only", "GFDL-1.2-or-later", "GFDL-1.3-invariants-only", "GFDL-1.3-invariants-or-later", "GFDL-1.3-no-invariants-only", "GFDL-1.3-no-invariants-or-later", "GFDL-1.3-only", "GFDL-1.3-or-later", "Giftware", "GL2PS", "Glide", "Glulxe", "GLWTPL", "gnuplot", "GPL-1.0-only", "GPL-1.0-or-later", "GPL-2.0-only", "GPL-2.0-or-later", "GPL-3.0-only", "GPL-3.0-or-later", "Graphics-Gems", "gSOAP-1.3b", "gtkbook", "Gutmann", "HaskellReport", "HDF5", "hdparm", "HIDAPI", "Hippocratic-2.1", "HP-1986", "HP-1989", "HPND", "HPND-DEC", "HPND-doc", "HPND-doc-sell", "HPND-export-US", "HPND-export-US-acknowledgement", "HPND-export-US-modify", "HPND-export2-US", "HPND-Fenneberg-Livingston", "HPND-INRIA-IMAG", "HPND-Intel", "HPND-Kevlin-Henney", "HPND-Markus-Kuhn", "HPND-merchantability-variant", "HPND-MIT-disclaimer", "HPND-Netrek", "HPND-Pbmplus", "HPND-sell-MIT-disclaimer-xserver", "HPND-sell-regexpr", "HPND-sell-variant", "HPND-sell-variant-MIT-disclaimer", "HPND-sell-variant-MIT-disclaimer-rev", "HPND-UC", "HPND-UC-export-US", "HTMLTIDY", "IBM-pibs", "ICU", "IEC-Code-Components-EULA", "IJG", "IJG-short", "ImageMagick", "iMatix", "Imlib2", "Info-ZIP", "Inner-Net-2.0", "InnoSetup", "Intel", "Intel-ACPI", "Interbase-1.0", "IPA", "IPL-1.0", "ISC", "ISC-Veillard", "Jam", "JasPer-2.0", "jove", "JPL-image", "JPNIC", "JSON", "Kastrup", "Kazlib", "Knuth-CTAN", "LAL-1.2", "LAL-1.3", "Latex2e", "Latex2e-translated-notice", "Leptonica", "LGPL-2.0-only", "LGPL-2.0-or-later", "LGPL-2.1-only", "LGPL-2.1-or-later", "LGPL-3.0-only", "LGPL-3.0-or-later", "LGPLLR", "Libpng", "libpng-1.6.35", "libpng-2.0", "libselinux-1.0", "libtiff", "libutil-David-Nugent", "LiLiQ-P-1.1", "LiLiQ-R-1.1", "LiLiQ-Rplus-1.1", "Linux-man-pages-1-para", "Linux-man-pages-copyleft", "Linux-man-pages-copyleft-2-para", "Linux-man-pages-copyleft-var", "Linux-OpenIB", "LOOP", "LPD-document", "LPL-1.0", "LPL-1.02", "LPPL-1.0", "LPPL-1.1", "LPPL-1.2", "LPPL-1.3a", "LPPL-1.3c", "lsof", "Lucida-Bitmap-Fonts", "LZMA-SDK-9.11-to-9.20", "LZMA-SDK-9.22", "Mackerras-3-Clause", "Mackerras-3-Clause-acknowledgment", "magaz", "mailprio", "MakeIndex", "man2html", "Martin-Birgmeier", "McPhee-slideshow", "metamail", "Minpack", "MIPS", "MirOS", "MIT", "MIT-0", "MIT-advertising", "MIT-Click", "MIT-CMU", "MIT-enna", "MIT-feh", "MIT-Festival", "MIT-Khronos-old", "MIT-Modern-Variant", "MIT-open-group", "MIT-testregex", "MIT-Wu", "MITNFA", "MMIXware", "Motosoto", "MPEG-SSG", "mpi-permissive", "mpich2", "MPL-1.0", "MPL-1.1", "MPL-2.0", "MPL-2.0-no-copyleft-exception", "mplus", "MS-LPL", "MS-PL", "MS-RL", "MTLL", "MulanPSL-1.0", "MulanPSL-2.0", "Multics", "Mup", "NAIST-2003", "NASA-1.3", "Naumen", "NBPL-1.0", "NCBI-PD", "NCGL-UK-2.0", "NCL", "NCSA", "NetCDF", "Newsletr", "NGPL", "ngrep", "NICTA-1.0", "NIST-PD", "NIST-PD-fallback", "NIST-Software", "NLOD-1.0", "NLOD-2.0", "NLPL", "Nokia", "NOSL", "Noweb", "NPL-1.0", "NPL-1.1", "NPOSL-3.0", "NRL", "NTIA-PD", "NTP", "NTP-0", "O-UDA-1.0", "OAR", "OCCT-PL", "OCLC-2.0", "ODbL-1.0", "ODC-By-1.0", "OFFIS", "OFL-1.0", "OFL-1.0-no-RFN", "OFL-1.0-RFN", "OFL-1.1", "OFL-1.1-no-RFN", "OFL-1.1-RFN", "OGC-1.0", "OGDL-Taiwan-1.0", "OGL-Canada-2.0", "OGL-UK-1.0", "OGL-UK-2.0", "OGL-UK-3.0", "OGTSL", "OLDAP-1.1", "OLDAP-1.2", "OLDAP-1.3", "OLDAP-1.4", "OLDAP-2.0", "OLDAP-2.0.1", "OLDAP-2.1", "OLDAP-2.2", "OLDAP-2.2.1", "OLDAP-2.2.2", "OLDAP-2.3", "OLDAP-2.4", "OLDAP-2.5", "OLDAP-2.6", "OLDAP-2.7", "OLDAP-2.8", "OLFL-1.3", "OML", "OpenPBS-2.3", "OpenSSL", "OpenSSL-standalone", "OpenVision", "OPL-1.0", "OPL-UK-3.0", "OPUBL-1.0", "OSET-PL-2.1", "OSL-1.0", "OSL-1.1", "OSL-2.0", "OSL-2.1", "OSL-3.0", "PADL", "Parity-6.0.0", "Parity-7.0.0", "PDDL-1.0", "PHP-3.0", "PHP-3.01", "Pixar", "pkgconf", "Plexus", "pnmstitch", "PolyForm-Noncommercial-1.0.0", "PolyForm-Small-Business-1.0.0", "PostgreSQL", "PPL", "PSF-2.0", "psfrag", "psutils", "Python-2.0", "Python-2.0.1", "python-ldap", "Qhull", "QPL-1.0", "QPL-1.0-INRIA-2004", "radvd", "Rdisc", "RHeCos-1.1", "RPL-1.1", "RPL-1.5", "RPSL-1.0", "RSA-MD", "RSCPL", "Ruby", "Ruby-pty", "SAX-PD", "SAX-PD-2.0", "Saxpath", "SCEA", "SchemeReport", "Sendmail", "Sendmail-8.23", "Sendmail-Open-Source-1.1", "SGI-B-1.0", "SGI-B-1.1", "SGI-B-2.0", "SGI-OpenGL", "SGP4", "SHL-0.5", "SHL-0.51", "SimPL-2.0", "SISSL", "SISSL-1.2", "SL", "Sleepycat", "SMAIL-GPL", "SMLNJ", "SMPPL", "SNIA", "snprintf", "SOFA", "softSurfer", "Soundex", "Spencer-86", "Spencer-94", "Spencer-99", "SPL-1.0", "ssh-keyscan", "SSH-OpenSSH", "SSH-short", "SSLeay-standalone", "SSPL-1.0", "SugarCRM-1.1.3", "SUL-1.0", "Sun-PPP", "Sun-PPP-2000", "SunPro", "SWL", "swrule", "Symlinks", "TAPR-OHL-1.0", "TCL", "TCP-wrappers", "TermReadKey", "TGPPL-1.0", "ThirdEye", "threeparttable", "TMate", "TORQUE-1.1", "TOSL", "TPDL", "TPL-1.0", "TrustedQSL", "TTWL", "TTYP0", "TU-Berlin-1.0", "TU-Berlin-2.0", "Ubuntu-font-1.0", "UCAR", "UCL-1.0", "ulem", "UMich-Merit", "Unicode-3.0", "Unicode-DFS-2015", "Unicode-DFS-2016", "Unicode-TOU", "UnixCrypt", "Unlicense", "Unlicense-libtelnet", "Unlicense-libwhirlpool", "UPL-1.0", "URT-RLE", "Vim", "VOSTROM", "VSL-1.0", "W3C", "W3C-19980720", "W3C-20150513", "w3m", "Watcom-1.0", "Widget-Workshop", "Wsuipa", "WTFPL", "wwl", "X11", "X11-distribute-modifications-variant", "X11-swapped", "Xdebug-1.03", "Xerox", "Xfig", "XFree86-1.1", "xinetd", "xkeyboard-config-Zinoviev", "xlock", "Xnet", "xpp", "XSkat", "xzoom", "YPL-1.0", "YPL-1.1", "Zed", "Zeeff", "Zend-2.0", "Zimbra-1.3", "Zimbra-1.4", "Zlib", "zlib-acknowledgement", "ZPL-1.1", "ZPL-2.0", "ZPL-2.1" ], "title": "LicenseId", "type": "string" }, { "enum": [ "AGPL-1.0", "AGPL-3.0", "BSD-2-Clause-FreeBSD", "BSD-2-Clause-NetBSD", "bzip2-1.0.5", "eCos-2.0", "GFDL-1.1", "GFDL-1.2", "GFDL-1.3", "GPL-1.0", "GPL-1.0+", "GPL-2.0", "GPL-2.0+", "GPL-2.0-with-autoconf-exception", "GPL-2.0-with-bison-exception", "GPL-2.0-with-classpath-exception", "GPL-2.0-with-font-exception", "GPL-2.0-with-GCC-exception", "GPL-3.0", "GPL-3.0+", "GPL-3.0-with-autoconf-exception", "GPL-3.0-with-GCC-exception", "LGPL-2.0", "LGPL-2.0+", "LGPL-2.1", "LGPL-2.1+", "LGPL-3.0", "LGPL-3.0+", "Net-SNMP", "Nunit", "StandardML-NJ", "wxWindows" ], "title": "DeprecatedLicenseId", "type": "string" }, { "type": "null" } ], "default": null, "description": "A [SPDX license identifier](https://spdx.org/licenses/).\nWe do not support custom license beyond the SPDX license list, if you need that please\n[open a GitHub issue](https://github.com/bioimage-io/spec-bioimage-io/issues/new/choose)\nto discuss your intentions with the community.", "examples": [ "CC0-1.0", "MIT", "BSD-2-Clause" ], "title": "License" }, "git_repo": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "type": "null" } ], "default": null, "description": "A URL to the Git repository where the resource is being developed.", "examples": [ "https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad" ], "title": "Git Repo" }, "icon": { "anyOf": [ { "maxLength": 2, "minLength": 1, "type": "string" }, { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "type": "null" } ], "default": null, "description": "An icon for illustration, e.g. on bioimage.io", "title": "Icon" }, "links": { "description": "IDs of other bioimage.io resources", "examples": [ [ "ilastik/ilastik", "deepimagej/deepimagej", "zero/notebook_u-net_3d_zerocostdl4mic" ] ], "items": { "type": "string" }, "title": "Links", "type": "array" }, "uploader": { "anyOf": [ { "$ref": "#/$defs/Uploader" }, { "type": "null" } ], "default": null, "description": "The person who uploaded the model (e.g. to bioimage.io)" }, "maintainers": { "description": "Maintainers of this resource.\nIf not specified, `authors` are maintainers and at least some of them has to specify their `github_user` name", "items": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Maintainer" }, "title": "Maintainers", "type": "array" }, "tags": { "description": "Associated tags", "examples": [ [ "unet2d", "pytorch", "nucleus", "segmentation", "dsb2018" ] ], "items": { "type": "string" }, "title": "Tags", "type": "array" }, "version": { "anyOf": [ { "$ref": "#/$defs/Version" }, { "type": "null" } ], "default": null, "description": "The version of the resource following SemVer 2.0." }, "version_comment": { "anyOf": [ { "maxLength": 512, "type": "string" }, { "type": "null" } ], "default": null, "description": "A comment on the version of the resource.", "title": "Version Comment" }, "format_version": { "const": "0.3.0", "description": "The **format** version of this resource specification", "title": "Format Version", "type": "string" }, "documentation": { "anyOf": [ { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" }, { "format": "file-path", "title": "FilePath", "type": "string" } ], "examples": [ "https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md", "README.md" ] }, { "type": "null" } ], "default": null, "description": "URL or relative path to a markdown file encoded in UTF-8 with additional documentation.\nThe recommended documentation file name is `README.md`. An `.md` suffix is mandatory.", "title": "Documentation" }, "badges": { "description": "badges associated with this resource", "items": { "$ref": "#/$defs/BadgeDescr" }, "title": "Badges", "type": "array" }, "config": { "$ref": "#/$defs/bioimageio__spec__generic__v0_3__Config", "description": "A field for custom configuration that can contain any keys not present in the RDF spec.\nThis means you should not store, for example, a GitHub repo URL in `config` since there is a `git_repo` field.\nKeys in `config` may be very specific to a tool or consumer software. To avoid conflicting definitions,\nit is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,\nfor example:\n```yaml\nconfig:\n giraffe_neckometer: # here is the domain name\n length: 3837283\n address:\n home: zoo\n imagej: # config specific to ImageJ\n macro_dir: path/to/macro/file\n```\nIf possible, please use [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) for keys in `config`.\nYou may want to list linked files additionally under `attachments` to include them when packaging a resource.\n(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains\nan altered rdf.yaml file with local references to the downloaded files.)" }, "type": { "const": "notebook", "title": "Type", "type": "string" }, "id": { "anyOf": [ { "minLength": 1, "title": "NotebookId", "type": "string" }, { "type": "null" } ], "default": null, "description": "bioimage.io-wide unique resource identifier\nassigned by bioimage.io; version **un**specific.", "title": "Id" }, "parent": { "anyOf": [ { "minLength": 1, "title": "NotebookId", "type": "string" }, { "type": "null" } ], "default": null, "description": "The description from which this one is derived", "title": "Parent" }, "source": { "anyOf": [ { "description": "A URL with the HTTP or HTTPS scheme.", "format": "uri", "maxLength": 2083, "minLength": 1, "title": "HttpUrl", "type": "string" }, { "format": "file-path", "title": "FilePath", "type": "string" }, { "$ref": "#/$defs/RelativeFilePath" } ], "description": "The Jupyter notebook", "title": "Source" } }, "required": [ "name", "format_version", "type", "source" ], "title": "notebook 0.3.0", "additionalProperties": false } }, "discriminator": { "mapping": { "application": { "discriminator": { "mapping": { "0.2.4": "#/$defs/bioimageio__spec__application__v0_2__ApplicationDescr", "0.3.0": "#/$defs/bioimageio__spec__application__v0_3__ApplicationDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__application__v0_2__ApplicationDescr", "title": "application 0.2" }, { "$ref": "#/$defs/bioimageio__spec__application__v0_3__ApplicationDescr", "title": "application 0.3" } ], "title": "application" }, "dataset": { "discriminator": { "mapping": { "0.2.4": "#/$defs/bioimageio__spec__dataset__v0_2__DatasetDescr", "0.3.0": "#/$defs/bioimageio__spec__dataset__v0_3__DatasetDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__dataset__v0_2__DatasetDescr", "title": "dataset 0.2" }, { "$ref": "#/$defs/bioimageio__spec__dataset__v0_3__DatasetDescr", "title": "dataset 0.3" } ], "title": "dataset" }, "model": { "discriminator": { "mapping": { "0.4.10": "#/$defs/bioimageio__spec__model__v0_4__ModelDescr", "0.5.9": "#/$defs/bioimageio__spec__model__v0_5__ModelDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ModelDescr", "title": "model 0.4" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ModelDescr", "title": "model 0.5" } ], "title": "model" }, "notebook": { "discriminator": { "mapping": { "0.2.4": "#/$defs/bioimageio__spec__notebook__v0_2__NotebookDescr", "0.3.0": "#/$defs/bioimageio__spec__notebook__v0_3__NotebookDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__notebook__v0_2__NotebookDescr", "title": "notebook 0.2" }, { "$ref": "#/$defs/bioimageio__spec__notebook__v0_3__NotebookDescr", "title": "notebook 0.3" } ], "title": "notebook" } }, "propertyName": "type" }, "oneOf": [ { "discriminator": { "mapping": { "0.2.4": "#/$defs/bioimageio__spec__application__v0_2__ApplicationDescr", "0.3.0": "#/$defs/bioimageio__spec__application__v0_3__ApplicationDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__application__v0_2__ApplicationDescr", "title": "application 0.2" }, { "$ref": "#/$defs/bioimageio__spec__application__v0_3__ApplicationDescr", "title": "application 0.3" } ], "title": "application" }, { "discriminator": { "mapping": { "0.2.4": "#/$defs/bioimageio__spec__dataset__v0_2__DatasetDescr", "0.3.0": "#/$defs/bioimageio__spec__dataset__v0_3__DatasetDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__dataset__v0_2__DatasetDescr", "title": "dataset 0.2" }, { "$ref": "#/$defs/bioimageio__spec__dataset__v0_3__DatasetDescr", "title": "dataset 0.3" } ], "title": "dataset" }, { "discriminator": { "mapping": { "0.4.10": "#/$defs/bioimageio__spec__model__v0_4__ModelDescr", "0.5.9": "#/$defs/bioimageio__spec__model__v0_5__ModelDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__model__v0_4__ModelDescr", "title": "model 0.4" }, { "$ref": "#/$defs/bioimageio__spec__model__v0_5__ModelDescr", "title": "model 0.5" } ], "title": "model" }, { "discriminator": { "mapping": { "0.2.4": "#/$defs/bioimageio__spec__notebook__v0_2__NotebookDescr", "0.3.0": "#/$defs/bioimageio__spec__notebook__v0_3__NotebookDescr" }, "propertyName": "format_version" }, "oneOf": [ { "$ref": "#/$defs/bioimageio__spec__notebook__v0_2__NotebookDescr", "title": "notebook 0.2" }, { "$ref": "#/$defs/bioimageio__spec__notebook__v0_3__NotebookDescr", "title": "notebook 0.3" } ], "title": "notebook" } ] }