Bioimage.io description of an application.
No Additional PropertiesA human-friendly name of the resource description
Must be at least 1 characters long
Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.
The supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
['cover.png']
UTF-8 emoji for display alongside the id.
Must be at least 1 characters long
Must be at most 1 characters long
🦈
🦥
file and other attachments
File attachments
No Additional ItemsA URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Additional Properties of any type are allowed.
Type: objectcitations
No Additional Itemsfree text description
A digital object identifier (DOI) is the prefered citation reference.
See https://www.doi.org/ for details. (alternatively specify url)
A digital object identifier, see https://www.doi.org/
Must match regular expression:^10\.[0-9]{4}.+$
URL to cite (preferably specify a doi instead)
A field for custom configuration that can contain any keys not present in the RDF spec.
This means you should not store, for example, a github repo URL in config since we already have the
git_repo field defined in the spec.
Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions,
it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,
for example:
config:
bioimageio: # here is the domain name
my_custom_key: 3837283
another_key:
nested: value
imagej: # config specific to ImageJ
macro_dir: path/to/macro/file
If possible, please use <code>snake_case</code> for keys in config.
You may want to list linked files additionally under attachments to include them when packaging a resource
(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains
an altered rdf.yaml file with local references to the downloaded files)
bioimageio:
another_key:
nested: value
my_custom_key: 3837283
imagej:
macro_dir: path/to/macro/file
Each additional property must conform to the following schema
Type: objectEach additional property must conform to the following schema
Type: objectURL to download the resource from (deprecated)
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A URL to the Git repository where the resource is being developed.
https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad
An icon for illustration
Must be at least 1 characters long
Must be at most 2 characters long
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
IDs of other bioimage.io resources
No Additional Items['ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic']
The person who uploaded the model (e.g. to bioimage.io)
name
Maintainers of this resource.
If not specified authors are maintainers and at least some of them should specify their github_user name
Affiliation
Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.
Do not set this field in a YAML file.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
The version of the resource following SemVer 2.0.
wraps a packaging.version.Version instance for validation in pydantic models
version number (n-th published version, not the semantic version)
The format version of this resource specification
(not the version of the resource description)
When creating a new resource always use the latest micro/patch version described here.
The format_version is important for any consumer software to understand how to parse the fields.
"0.2.4"
badges associated with this resource
No Additional ItemsA custom badge
No Additional Propertiesbadge label to display on hover
Open in Colab
badge icon (included in bioimage.io package if not a URL)
A path relative to the rdf.yaml file (also if the RDF source is a URL).
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/assets/colab-badge.svg
target URL
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb
URL or relative path to a markdown file with additional documentation.
The recommended documentation file name is README.md. An .md suffix is mandatory.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md
README.md
A SPDX license identifier.
We do not support custom license beyond the SPDX license list, if you need that please
open a GitHub issue to discuss your intentions with the community.
CC0-1.0
MIT
BSD-2-Clause
"application"
bioimage.io-wide unique resource identifier
assigned by bioimage.io; version unspecific.
Must be at least 1 characters long
URL or path to the source of the application
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Bioimage.io description of an application.
No Additional PropertiesA human-friendly name of the resource description.
May only contains letters, digits, underscore, minus, parentheses and spaces.
Must be at least 5 characters long
Must be at most 128 characters long
A string containing a brief description.
Must be at most 1024 characters long
Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.
The supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
['cover.png']
UTF-8 emoji for display alongside the id.
Must be at least 1 characters long
Must be at most 2 characters long
🦈
🦥
file attachments
No Additional ItemsA file description
No Additional PropertiesFile source
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
SHA256 hash value of the source file.
A SHA-256 hash value
Must be at least 64 characters long
Must be at most 64 characters long
citations
No Additional ItemsA citation that should be referenced in work using this resource.
No Additional Propertiesfree text description
A digital object identifier (DOI) is the prefered citation reference.
See https://www.doi.org/ for details.
Note:
Either doi or url have to be specified.
A digital object identifier, see https://www.doi.org/
Must match regular expression:^10\.[0-9]{4}.+$
URL to cite (preferably specify a doi instead/also).
Note:
Either doi or url have to be specified.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A SPDX license identifier.
We do not support custom license beyond the SPDX license list, if you need that please
open a GitHub issue
to discuss your intentions with the community.
CC0-1.0
MIT
BSD-2-Clause
A URL to the Git repository where the resource is being developed.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad
An icon for illustration, e.g. on bioimage.io
Must be at least 1 characters long
Must be at most 2 characters long
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
IDs of other bioimage.io resources
No Additional Items['ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic']
The person who uploaded the model (e.g. to bioimage.io)
name
Maintainers of this resource.
If not specified, authors are maintainers and at least some of them has to specify their github_user name
Affiliation
The version of the resource following SemVer 2.0.
wraps a packaging.version.Version instance for validation in pydantic models
A comment on the version of the resource.
Must be at most 512 characters long
The format version of this resource specification
Specific value:"0.3.0"
URL or relative path to a markdown file encoded in UTF-8 with additional documentation.
The recommended documentation file name is README.md. An .md suffix is mandatory.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md
README.md
badges associated with this resource
No Additional ItemsA custom badge
No Additional Propertiesbadge label to display on hover
Open in Colab
badge icon (included in bioimage.io package if not a URL)
A path relative to the rdf.yaml file (also if the RDF source is a URL).
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/assets/colab-badge.svg
target URL
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb
A field for custom configuration that can contain any keys not present in the RDF spec.
This means you should not store, for example, a GitHub repo URL in config since there is a git_repo field.
Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions,
it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,
for example:
config:
giraffe_neckometer: # here is the domain name
length: 3837283
address:
home: zoo
imagej: # config specific to ImageJ
macro_dir: path/to/macro/file
If possible, please use <code>snake_case</code> for keys in config.
You may want to list linked files additionally under attachments to include them when packaging a resource.
(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains
an altered rdf.yaml file with local references to the downloaded files.)
bioimage.io internal metadata.
Additional Properties of any type are allowed.
Type: objectAdditional Properties of any type are allowed.
Type: object"application"
bioimage.io-wide unique resource identifier
assigned by bioimage.io; version unspecific.
Must be at least 1 characters long
The description from which this one is derived
Must be at least 1 characters long
URL or path to the source of the application
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
processing.
A human-friendly name of the resource description
Must be at least 1 characters long
Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.
The supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
['cover.png']
UTF-8 emoji for display alongside the id.
Must be at least 1 characters long
Must be at most 1 characters long
🦈
🦥
file and other attachments
File attachments
No Additional ItemsA URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Additional Properties of any type are allowed.
Type: objectcitations
No Additional Itemsfree text description
A digital object identifier (DOI) is the prefered citation reference.
See https://www.doi.org/ for details. (alternatively specify url)
A digital object identifier, see https://www.doi.org/
Must match regular expression:^10\.[0-9]{4}.+$
URL to cite (preferably specify a doi instead)
A field for custom configuration that can contain any keys not present in the RDF spec.
This means you should not store, for example, a github repo URL in config since we already have the
git_repo field defined in the spec.
Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions,
it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,
for example:
config:
bioimageio: # here is the domain name
my_custom_key: 3837283
another_key:
nested: value
imagej: # config specific to ImageJ
macro_dir: path/to/macro/file
If possible, please use <code>snake_case</code> for keys in config.
You may want to list linked files additionally under attachments to include them when packaging a resource
(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains
an altered rdf.yaml file with local references to the downloaded files)
bioimageio:
another_key:
nested: value
my_custom_key: 3837283
imagej:
macro_dir: path/to/macro/file
Each additional property must conform to the following schema
Type: objectEach additional property must conform to the following schema
Type: objectURL to download the resource from (deprecated)
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A URL to the Git repository where the resource is being developed.
https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad
An icon for illustration
Must be at least 1 characters long
Must be at most 2 characters long
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
IDs of other bioimage.io resources
No Additional Items['ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic']
The person who uploaded the model (e.g. to bioimage.io)
name
Maintainers of this resource.
If not specified authors are maintainers and at least some of them should specify their github_user name
Affiliation
Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.
Do not set this field in a YAML file.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
The version of the resource following SemVer 2.0.
wraps a packaging.version.Version instance for validation in pydantic models
version number (n-th published version, not the semantic version)
The format version of this resource specification
(not the version of the resource description)
When creating a new resource always use the latest micro/patch version described here.
The format_version is important for any consumer software to understand how to parse the fields.
"0.2.4"
badges associated with this resource
No Additional ItemsA custom badge
No Additional Propertiesbadge label to display on hover
Open in Colab
badge icon (included in bioimage.io package if not a URL)
A path relative to the rdf.yaml file (also if the RDF source is a URL).
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/assets/colab-badge.svg
target URL
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb
URL or relative path to a markdown file with additional documentation.
The recommended documentation file name is README.md. An .md suffix is mandatory.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md
README.md
A SPDX license identifier.
We do not support custom license beyond the SPDX license list, if you need that please
open a GitHub issue to discuss your intentions with the community.
CC0-1.0
MIT
BSD-2-Clause
"dataset"
bioimage.io-wide unique resource identifier
assigned by bioimage.io; version unspecific.
Must be at least 1 characters long
"URL to the source of the dataset.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
processing.
A human-friendly name of the resource description.
May only contains letters, digits, underscore, minus, parentheses and spaces.
Must be at least 5 characters long
Must be at most 128 characters long
A string containing a brief description.
Must be at most 1024 characters long
Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1 or 1:1.
The supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg')
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
['cover.png']
UTF-8 emoji for display alongside the id.
Must be at least 1 characters long
Must be at most 2 characters long
🦈
🦥
file attachments
No Additional ItemsA file description
No Additional PropertiesFile source
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
SHA256 hash value of the source file.
A SHA-256 hash value
Must be at least 64 characters long
Must be at most 64 characters long
citations
No Additional ItemsA citation that should be referenced in work using this resource.
No Additional Propertiesfree text description
A digital object identifier (DOI) is the prefered citation reference.
See https://www.doi.org/ for details.
Note:
Either doi or url have to be specified.
A digital object identifier, see https://www.doi.org/
Must match regular expression:^10\.[0-9]{4}.+$
URL to cite (preferably specify a doi instead/also).
Note:
Either doi or url have to be specified.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A SPDX license identifier.
We do not support custom license beyond the SPDX license list, if you need that please
open a GitHub issue
to discuss your intentions with the community.
CC0-1.0
MIT
BSD-2-Clause
A URL to the Git repository where the resource is being developed.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad
An icon for illustration, e.g. on bioimage.io
Must be at least 1 characters long
Must be at most 2 characters long
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
IDs of other bioimage.io resources
No Additional Items['ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic']
The person who uploaded the model (e.g. to bioimage.io)
name
Maintainers of this resource.
If not specified, authors are maintainers and at least some of them has to specify their github_user name
Affiliation
The version of the resource following SemVer 2.0.
wraps a packaging.version.Version instance for validation in pydantic models
A comment on the version of the resource.
Must be at most 512 characters long
The format version of this resource specification
Specific value:"0.3.0"
URL or relative path to a markdown file encoded in UTF-8 with additional documentation.
The recommended documentation file name is README.md. An .md suffix is mandatory.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md
README.md
badges associated with this resource
No Additional ItemsA custom badge
No Additional Propertiesbadge label to display on hover
Open in Colab
badge icon (included in bioimage.io package if not a URL)
A path relative to the rdf.yaml file (also if the RDF source is a URL).
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/assets/colab-badge.svg
target URL
Must be at least 1 characters long
Must be at most 2083 characters long
https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb
A field for custom configuration that can contain any keys not present in the RDF spec.
This means you should not store, for example, a GitHub repo URL in config since there is a git_repo field.
Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions,
it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,
for example:
config:
giraffe_neckometer: # here is the domain name
length: 3837283
address:
home: zoo
imagej: # config specific to ImageJ
macro_dir: path/to/macro/file
If possible, please use <code>snake_case</code> for keys in config.
You may want to list linked files additionally under attachments to include them when packaging a resource.
(Packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains
an altered rdf.yaml file with local references to the downloaded files.)
bioimage.io internal metadata.
Additional Properties of any type are allowed.
Type: objectAdditional Properties of any type are allowed.
Type: object"dataset"
bioimage.io-wide unique resource identifier
assigned by bioimage.io; version unspecific.
Must be at least 1 characters long
The description from which this one is derived
Must be at least 1 characters long
"URL to the source of the dataset.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
Specification of the fields used in a bioimage.io-compliant RDF that describes AI models with pretrained weights.
These fields are typically stored in a YAML file which we call a model resource description file (model RDF).
No Additional PropertiesA human-readable name of this model.
It should be no longer than 64 characters and only contain letter, number, underscore, minus or space characters.
Must be at least 1 characters long
Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.
The supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
['cover.png']
UTF-8 emoji for display alongside the id.
Must be at least 1 characters long
Must be at most 1 characters long
🦈
🦥
file and other attachments
File attachments
No Additional ItemsA URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Additional Properties of any type are allowed.
Type: objectcitations
No Additional Itemsfree text description
A digital object identifier (DOI) is the prefered citation reference.
See https://www.doi.org/ for details. (alternatively specify url)
A digital object identifier, see https://www.doi.org/
Must match regular expression:^10\.[0-9]{4}.+$
URL to cite (preferably specify a doi instead)
A field for custom configuration that can contain any keys not present in the RDF spec.
This means you should not store, for example, a github repo URL in config since we already have the
git_repo field defined in the spec.
Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions,
it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,
for example:
config:
bioimageio: # here is the domain name
my_custom_key: 3837283
another_key:
nested: value
imagej: # config specific to ImageJ
macro_dir: path/to/macro/file
If possible, please use <code>snake_case</code> for keys in config.
You may want to list linked files additionally under attachments to include them when packaging a resource
(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains
an altered rdf.yaml file with local references to the downloaded files)
bioimageio:
another_key:
nested: value
my_custom_key: 3837283
imagej:
macro_dir: path/to/macro/file
Each additional property must conform to the following schema
Type: objectEach additional property must conform to the following schema
Type: objectURL to download the resource from (deprecated)
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A URL to the Git repository where the resource is being developed.
https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad
An icon for illustration
Must be at least 1 characters long
Must be at most 2 characters long
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
IDs of other bioimage.io resources
No Additional Items['ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic']
The person who uploaded the model (e.g. to bioimage.io)
name
Maintainers of this resource.
If not specified authors are maintainers and at least some of them should specify their github_user name
Affiliation
Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.
Do not set this field in a YAML file.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
The version of the resource following SemVer 2.0.
wraps a packaging.version.Version instance for validation in pydantic models
version number (n-th published version, not the semantic version)
Version of the bioimage.io model description specification used.
When creating a new model always use the latest micro/patch version described here.
The format_version is important for any consumer software to understand how to parse the fields.
"0.4.10"
Specialized resource type 'model'
Specific value:"model"
bioimage.io-wide unique resource identifier
assigned by bioimage.io; version unspecific.
Must be at least 1 characters long
URL or relative path to a markdown file with additional documentation.
The recommended documentation file name is README.md. An .md suffix is mandatory.
The documentation should include a '[#[#]]# Validation' (sub)section
with details on how to quantitatively validate the model on unseen data.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md
README.md
Describes the input tensors expected by this model.
Must contain a minimum of 1 items
Tensor name. No duplicates are allowed.
Must be at least 1 characters long
Tuple (minimum, maximum) specifying the allowed range of the data in this tensor.
If not specified, the full data range that can be expressed in data_type is allowed.
Must contain a minimum of 2 items
Must contain a maximum of 2 items
For now an input tensor is expected to be given as float32.
The data flow in bioimage.io models is explained
in this diagram..
Specification of input tensor shape.
A sequence of valid shapes given by shape_k = min + k * step for k in {0, 1, ...}.
The minimum input shape
Must contain a minimum of 1 items
The minimum shape change
Must contain a minimum of 1 items
[1, 512, 512, 1]
min:
- 1
- 64
- 64
- 1
step:
- 0
- 32
- 32
- 0
Description of how this input should be preprocessed.
No Additional ItemsBinarizeDescr the tensor with a fixed BinarizeKwargs.threshold.
Values above the threshold will be set to one, values below the threshold to zero.
"binarize"
key word arguments for BinarizeDescr
The fixed threshold
Clip tensor values to a range.
Set tensor values below ClipKwargs.min to ClipKwargs.min
and above ClipKwargs.max to ClipKwargs.max.
"clip"
key word arguments for ClipDescr
minimum value for clipping
maximum value for clipping
Fixed linear scaling.
No Additional Properties"scale_linear"
key word arguments for ScaleLinearDescr
The subset of axes to scale jointly.
For example xy to scale the two image axes for 2d data jointly.
xy
multiplicative factor
additive term
The logistic sigmoid funciton, a.k.a. expit function.
No Additional Properties"sigmoid"
Subtract mean and divide by variance.
No Additional Properties"zero_mean_unit_variance"
key word arguments for ZeroMeanUnitVarianceDescr
The subset of axes to normalize jointly.
For example xy to normalize the two image axes for 2d data jointly.
xy
The mean value(s) to use for mode: fixed.
For example [1.1, 2.2, 3.3] in the case of a 3 channel image with axes: xy.
Must contain a minimum of 1 items
[1.1, 2.2, 3.3]
The standard deviation values to use for mode: fixed. Analogous to mean.
Must contain a minimum of 1 items
[0.1, 0.2, 0.3]
epsilon for numeric stability: out = (tensor - mean) / (std + eps).
Value must be strictly greater than 0 and lesser or equal to 0.1
Scale with percentiles.
No Additional Properties"scale_range"
key word arguments for ScaleRangeDescr
For min_percentile=0.0 (the default) and max_percentile=100 (the default)
this processing step normalizes data to the [0, 1] intervall.
For other percentiles the normalized values will partially be outside the [0, 1]
intervall. Use ScaleRange followed by ClipDescr if you want to limit the
normalized values to a range.
The subset of axes to normalize jointly.
For example xy to normalize the two image axes for 2d data jointly.
xy
The lower percentile used to determine the value to align with zero.
The upper percentile used to determine the value to align with one.
Has to be bigger than min_percentile.
The range is 1 to 100 instead of 0 to 100 to avoid mistakenly
accepting percentiles specified in the range 0.0 to 1.0.
Epsilon for numeric stability.
out = (tensor - v_lower) / (v_upper - v_lower + eps);
with v_lower,v_upper values at the respective percentiles.
Value must be strictly greater than 0 and lesser or equal to 0.1
Tensor name to compute the percentiles from. Default: The tensor itself.
For any tensor in inputs only input tensor references are allowed.
For a tensor in outputs only input tensor refereences are allowed if mode: per_dataset
Must be at least 1 characters long
A SPDX license identifier.
We do notsupport custom license beyond the SPDX license list, if you need that please
open a GitHub issue to discuss your intentions with the community.
CC0-1.0
MIT
BSD-2-Clause
Describes the output tensors.
Must contain a minimum of 1 items
Tensor name. No duplicates are allowed.
Must be at least 1 characters long
Tuple (minimum, maximum) specifying the allowed range of the data in this tensor.
If not specified, the full data range that can be expressed in data_type is allowed.
Must contain a minimum of 2 items
Must contain a maximum of 2 items
Data type.
The data flow in bioimage.io models is explained
in this diagram..
Output tensor shape.
Output tensor shape depending on an input tensor shape.
shape(output_tensor) = shape(input_tensor) * scale + 2 * offset
Name of the reference tensor.
Must be at least 1 characters long
outputpix/inputpix for each dimension.
'null' values indicate new dimensions, whose length is defined by 2*offset
Must contain a minimum of 1 items
Position of origin wrt to input.
Must contain a minimum of 1 items
The halo that should be cropped from the output tensor to avoid boundary effects.
The halo is to be cropped from both sides, i.e. shape_after_crop = shape - 2 * halo.
To document a halo that is already cropped by the model shape.offset has to be used instead.
Description of how this output should be postprocessed.
No Additional ItemsBinarizeDescr the tensor with a fixed BinarizeKwargs.threshold.
Values above the threshold will be set to one, values below the threshold to zero.
"binarize"
key word arguments for BinarizeDescr
The fixed threshold
Clip tensor values to a range.
Set tensor values below ClipKwargs.min to ClipKwargs.min
and above ClipKwargs.max to ClipKwargs.max.
"clip"
key word arguments for ClipDescr
minimum value for clipping
maximum value for clipping
Fixed linear scaling.
No Additional Properties"scale_linear"
key word arguments for ScaleLinearDescr
The subset of axes to scale jointly.
For example xy to scale the two image axes for 2d data jointly.
xy
multiplicative factor
additive term
The logistic sigmoid funciton, a.k.a. expit function.
No Additional Properties"sigmoid"
Subtract mean and divide by variance.
No Additional Properties"zero_mean_unit_variance"
key word arguments for ZeroMeanUnitVarianceDescr
The subset of axes to normalize jointly.
For example xy to normalize the two image axes for 2d data jointly.
xy
The mean value(s) to use for mode: fixed.
For example [1.1, 2.2, 3.3] in the case of a 3 channel image with axes: xy.
Must contain a minimum of 1 items
[1.1, 2.2, 3.3]
The standard deviation values to use for mode: fixed. Analogous to mean.
Must contain a minimum of 1 items
[0.1, 0.2, 0.3]
epsilon for numeric stability: out = (tensor - mean) / (std + eps).
Value must be strictly greater than 0 and lesser or equal to 0.1
Scale with percentiles.
No Additional Properties"scale_range"
key word arguments for ScaleRangeDescr
For min_percentile=0.0 (the default) and max_percentile=100 (the default)
this processing step normalizes data to the [0, 1] intervall.
For other percentiles the normalized values will partially be outside the [0, 1]
intervall. Use ScaleRange followed by ClipDescr if you want to limit the
normalized values to a range.
The subset of axes to normalize jointly.
For example xy to normalize the two image axes for 2d data jointly.
xy
The lower percentile used to determine the value to align with zero.
The upper percentile used to determine the value to align with one.
Has to be bigger than min_percentile.
The range is 1 to 100 instead of 0 to 100 to avoid mistakenly
accepting percentiles specified in the range 0.0 to 1.0.
Epsilon for numeric stability.
out = (tensor - v_lower) / (v_upper - v_lower + eps);
with v_lower,v_upper values at the respective percentiles.
Value must be strictly greater than 0 and lesser or equal to 0.1
Tensor name to compute the percentiles from. Default: The tensor itself.
For any tensor in inputs only input tensor references are allowed.
For a tensor in outputs only input tensor refereences are allowed if mode: per_dataset
Must be at least 1 characters long
Scale the tensor s.t. its mean and variance match a reference tensor.
No Additional Properties"scale_mean_variance"
key word arguments for ScaleMeanVarianceDescr
Name of tensor to match.
Must be at least 1 characters long
The subset of axes to scale jointly.
For example xy to normalize the two image axes for 2d data jointly.
Default: scale all non-batch axes jointly.
xy
Epsilon for numeric stability:
"`out = (tensor - mean) / (std + eps) * (refstd + eps) + refmean.
Value must be strictly greater than 0 and lesser or equal to 0.1
The persons that have packaged and uploaded this model.
Only required if those persons differ from the authors.
Affiliation
The model from which this model is derived, e.g. by fine-tuning the weights.
Reference to a bioimage.io model.
No Additional PropertiesA valid model id from the bioimage.io collection.
Must be at least 1 characters long
affable-shark
ambitious-sloth
version number (n-th published version, not the semantic version) of linked model
Custom run mode for this model: for more complex prediction procedures like test time
data augmentation that currently cannot be expressed in the specification.
No standard run modes are defined yet.
Run mode name
"deepimagej"
Run mode specific key word arguments
Additional Properties of any type are allowed.
Type: objectURLs/relative paths to sample inputs to illustrate possible inputs for the model,
for example stored as PNG or TIFF images.
The sample files primarily serve to inform a human user about an example use case
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
URLs/relative paths to sample outputs corresponding to the sample_inputs.
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Test input tensors compatible with the inputs description for a single test case.
This means if your model has more than one input, you should provide one URL/relative path for each input.
Each test input should be a file with an ndarray in
numpy.lib file format.
The extension must be '.npy'.
Must contain a minimum of 1 items
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Analog to test_inputs.
Must contain a minimum of 1 items
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
The dataset used to train this model
Reference to a bioimage.io dataset.
No Additional PropertiesA valid dataset id from the bioimage.io collection.
Must be at least 1 characters long
version number (n-th published version, not the semantic version) of linked dataset
A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
processing.
A human-friendly name of the resource description
Must be at least 1 characters long
Cover images. Please use an image smaller than 500KB and an aspect ratio width to height of 2:1.
The supported image formats are: ('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff')
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
['cover.png']
UTF-8 emoji for display alongside the id.
Must be at least 1 characters long
Must be at most 1 characters long
🦈
🦥
file and other attachments
File attachments
No Additional ItemsA URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
Additional Properties of any type are allowed.
Type: objectcitations
No Additional Itemsfree text description
A digital object identifier (DOI) is the prefered citation reference.
See https://www.doi.org/ for details. (alternatively specify url)
A digital object identifier, see https://www.doi.org/
Must match regular expression:^10\.[0-9]{4}.+$
URL to cite (preferably specify a doi instead)
A field for custom configuration that can contain any keys not present in the RDF spec.
This means you should not store, for example, a github repo URL in config since we already have the
git_repo field defined in the spec.
Keys in config may be very specific to a tool or consumer software. To avoid conflicting definitions,
it is recommended to wrap added configuration into a sub-field named with the specific domain or tool name,
for example:
config:
bioimageio: # here is the domain name
my_custom_key: 3837283
another_key:
nested: value
imagej: # config specific to ImageJ
macro_dir: path/to/macro/file
If possible, please use <code>snake_case</code> for keys in config.
You may want to list linked files additionally under attachments to include them when packaging a resource
(packaging a resource means downloading/copying important linked files and creating a ZIP archive that contains
an altered rdf.yaml file with local references to the downloaded files)
bioimageio:
another_key:
nested: value
my_custom_key: 3837283
imagej:
macro_dir: path/to/macro/file
Each additional property must conform to the following schema
Type: objectEach additional property must conform to the following schema
Type: objectURL to download the resource from (deprecated)
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A URL to the Git repository where the resource is being developed.
https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad
An icon for illustration
Must be at least 1 characters long
Must be at most 2 characters long
A URL with the HTTP or HTTPS scheme.
Must be at least 1 characters long
Must be at most 2083 characters long
A path relative to the rdf.yaml file (also if the RDF source is a URL).
IDs of other bioimage.io resources
No Additional Items['ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic']
The person who uploaded the model (e.g. to bioimage.io)
name
Maintainers of this resource.
If not specified authors are maintainers and at least some of them should specify their github_user name
Affiliation
Resource description file (RDF) source; used to keep track of where an rdf.yaml was loaded from.
Do not set this field in a YAML file.