bioimage.io dataset specification

A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage processing.

General notes on this documentation:

symbol	explanation
`field`_{type hint}	A fields's _{expected type} may be shortened. If so, the abbreviated or full type is displayed below the field's description and can expanded to view further (nested) details if available.
Union[A, B, ...]	indicates that a field value may be of type A or B, etc.
Literal[a, b, ...]	indicates that a field value must be the specific value a or b, etc.
Type* := Type (restrictions)	A field Type* followed by an asterisk indicates that annotations, e.g. value restriction apply. These are listed in parentheses in the expanded type description. They are not always intuitively understandable and merely a hint at more complex validation.
<type>.v<major>_<minor>.<sub spec>	Subparts of a spec might be taken from another spec type or format version.
`field` ≝ `default`	Default field values are indicated after '≝' and make a field optional. However, `type` and `format_version` alwyas need to be set for resource descriptions written as YAML files and determine which bioimage.io specification applies. They are optional only when creating a resource description in Python code using the appropriate, `type` and `format_version` specific class.
`field` ≝ 🡇	Default field value is not displayed in-line, but in the code block below.
∈📦	Files referenced in fields which are marked with '∈📦 ' are included when packaging the resource to a .zip archive. The resource description YAML file (RDF) is always included well as 'rdf.yaml'.

`type`_{Literal[dataset]} ≝ `dataset`

`format_version`_{Literal[0.2.4]} ≝ `0.2.4`

`description`_str

`name`_str

`attachments`_Optional ≝ `None`

Optional[generic.v0_2.AttachmentsDescr]

generic.v0_2.AttachmentsDescr:

`attachments.files`_Sequence ≝ `[]`

Sequence[Union[Path*, _internal.io.RelativeFilePath, _internal.url.HttpUrl, Url*]*]

Sequence of Union of

Path (PathType(path_type='file'))
_internal.io.RelativeFilePath
_internal.url.HttpUrl
Url (max_length=2083 allowed_schemes=['http', 'https'])

(union_mode='left_to_right'; AfterValidator(wo_special_file_name); PlainSerializer(func=<function _package at 0x7fa1164f4540>, return_type=PydanticUndefined, when_used='unless-none'))

`authors`_{Sequence[generic.v0_2.Author]} ≝ `[]`

Sequence[generic.v0_2.Author]

generic.v0_2.Author:

`authors.i.affiliation`_{Optional[str]} ≝ `None`

`authors.i.email`_{Optional[Email]} ≝ `None`

`authors.i.orcid`_Optional ≝ `None`

Example: '0000-0001-2345-6789'

Optional[_internal.types.OrcidId]

`authors.i.name`_str

`authors.i.github_user`_{Optional[str]} ≝ `None`

`badges`_Sequence ≝ `[]`

Sequence[generic.v0_2.BadgeDescr]

generic.v0_2.BadgeDescr:

`badges.i.label`_str

Example: 'Open in Colab'

`badges.i.icon`_Union ≝ `None`

Example: 'https://colab.research.google.com/assets/colab-badge.svg'

Union[Union[Path*, _internal.io.RelativeFilePath]*, _internal.url.HttpUrl, Url*, None]

Union of

Union[Path (PathType(path_type='file')), _internal.io.RelativeFilePath] (AfterValidator(wo_special_file_name); PlainSerializer(func=<function _package at 0x7fa1164f4540>, return_type=PydanticUndefined, when_used='unless-none'))
_internal.url.HttpUrl
Url (max_length=2083 allowed_schemes=['http', 'https'])
None

`badges.i.url`_{_internal.url.HttpUrl}

Example: 'https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb'

`cite`_{Sequence[generic.v0_2.CiteEntry]} ≝ `[]`

Sequence[generic.v0_2.CiteEntry]

generic.v0_2.CiteEntry:

`cite.i.text`_str

`cite.i.doi`_{Optional[_internal.types.Doi]} ≝ `None`

`cite.i.url`_{Optional[str]} ≝ `None`

`config`_{Dict[str, YamlValue]} ≝ `{}`

Example: {'bioimageio': {'my_custom_key': 3837283, 'another_key': {'nested': 'value'}}, 'imagej': {'macro_dir': 'path/to/macro/file'}}

`covers`_Sequence ≝ `[]`

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') Example: 'cover.png'

Sequence[Union[Path*, _internal.io.RelativeFilePath, _internal.url.HttpUrl]*]

Sequence of Union of

Path (PathType(path_type='file'); Predicate(func=<function PurePath.is_absolute at 0x7fa119a63ba0>))
_internal.io.RelativeFilePath
_internal.url.HttpUrl

(union_mode='left_to_right'; WithSuffix(suffix=('.gif', '.jpeg', '.jpg', '.png', '.svg', '.tif', '.tiff'), case_sensitive=False); PlainSerializer(func=<function _package at 0x7fa1164f4540>, return_type=PydanticUndefined, when_used='unless-none'))

`documentation`_Optional ≝ `None`

Examples: ['https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md', '…']

Optional[Union[Path*, _internal.io.RelativeFilePath, _internal.url.HttpUrl, Url*]*]

Optional[Union of

Path (PathType(path_type='file'))
_internal.io.RelativeFilePath
_internal.url.HttpUrl
Url (max_length=2083 allowed_schemes=['http', 'https'])

(union_mode='left_to_right'; AfterValidator(wo_special_file_name); PlainSerializer(func=<function _package at 0x7fa1164f4540>, return_type=PydanticUndefined, when_used='unless-none'))]

`download_url`_{Optional[_internal.url.HttpUrl]} ≝ `None`

`git_repo`_{Optional[str]} ≝ `None`

Example: 'https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad'

`icon`_Union ≝ `None`

Union[str*, Union[Path*, _internal.io.RelativeFilePath, _internal.url.HttpUrl, Url*]*, None]

Union of

str (Len(min_length=1, max_length=2))
Union of
- Path (PathType(path_type='file'))
- _internal.io.RelativeFilePath
- _internal.url.HttpUrl
- Url (max_length=2083 allowed_schemes=['http', 'https'])
(union_mode='left_to_right'; AfterValidator(wo_special_file_name); PlainSerializer(func=<function _package at 0x7fa1164f4540>, return_type=PydanticUndefined, when_used='unless-none'))
None

`id`_{Optional[DatasetId]} ≝ `None`

`id_emoji`_Optional ≝ `None`

Optional[str (Len(min_length=1, max_length=1))]

`license`_Union ≝ `None`

Examples: ['CC0-1.0', 'MIT', 'BSD-2-Clause']

Union[_internal.license_id.LicenseId, _internal.license_id.DeprecatedLicenseId, str, None]

`links`_{Sequence[str]} ≝ `[]`

Example: ('ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic')

`maintainers`_Sequence ≝ `[]`

Sequence[generic.v0_2.Maintainer]

generic.v0_2.Maintainer:

`maintainers.i.affiliation`_{Optional[str]} ≝ `None`

`maintainers.i.email`_{Optional[Email]} ≝ `None`

`maintainers.i.orcid`_Optional ≝ `None`

Example: '0000-0001-2345-6789'

Optional[_internal.types.OrcidId]

`maintainers.i.name`_Optional ≝ `None`

Optional[str (AfterValidator(_remove_slashes))]

`maintainers.i.github_user`_str

`rdf_source`_Optional ≝ `None`

Optional[Union[Path*, _internal.io.RelativeFilePath, _internal.url.HttpUrl, Url*]*]

Optional[Union of

Path (PathType(path_type='file'))
_internal.io.RelativeFilePath
_internal.url.HttpUrl
Url (max_length=2083 allowed_schemes=['http', 'https'])

(union_mode='left_to_right')]

`source`_{Optional[_internal.url.HttpUrl]} ≝ `None`

`tags`_{Sequence[str]} ≝ `[]`

Example: ('unet2d', 'pytorch', 'nucleus', 'segmentation', 'dsb2018')

`uploader`_{Optional[generic.v0_2.Uploader]} ≝ `None`

Optional[generic.v0_2.Uploader]

generic.v0_2.Uploader:

`uploader.email`_Email

`uploader.name`_Optional ≝ `None`

Optional[str (AfterValidator(_remove_slashes))]

`version`_Optional ≝ `None`

Optional[_internal.version_type.Version]

`version_number`_{Optional[int]} ≝ `None`

Example values

`authors.i.orcid`

0000-0001-2345-6789

`badges.i.label`

Open in Colab

`badges.i.icon`

https://colab.research.google.com/assets/colab-badge.svg

`badges.i.url`

https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb

`config`

{'bioimageio': {'my_custom_key': 3837283, 'another_key': {'nested': 'value'}}, 'imagej': {'macro_dir': 'path/to/macro/file'}}

`covers`

cover.png

`documentation`

https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/example_descriptions/models/unet2d_nuclei_broad/README.md
README.md

`git_repo`

https://github.com/bioimage-io/spec-bioimage-io/tree/main/example_descriptions/models/unet2d_nuclei_broad

`license`

CC0-1.0
MIT
BSD-2-Clause

`links`

('ilastik/ilastik', 'deepimagej/deepimagej', 'zero/notebook_u-net_3d_zerocostdl4mic')

`maintainers.i.orcid`

0000-0001-2345-6789

`tags`

('unet2d', 'pytorch', 'nucleus', 'segmentation', 'dsb2018')

Files

dataset_descr_v0-2.md

Latest commit

History

dataset_descr_v0-2.md

File metadata and controls

bioimage.io dataset specification

type Literal[dataset] ≝ dataset

format_version Literal[0.2.4] ≝ 0.2.4

description str

name str

attachments Optional ≝ None

attachments.files Sequence ≝ []

authors Sequence[generic.v0_2.Author] ≝ []

authors.i.affiliation Optional[str] ≝ None

authors.i.email Optional[Email] ≝ None

authors.i.orcid Optional ≝ None

authors.i.name str

authors.i.github_user Optional[str] ≝ None

badges Sequence ≝ []

badges.i.label str

badges.i.icon Union ≝ None

badges.i.url _internal.url.HttpUrl

cite Sequence[generic.v0_2.CiteEntry] ≝ []

cite.i.text str

cite.i.doi Optional[_internal.types.Doi] ≝ None

cite.i.url Optional[str] ≝ None

config Dict[str, YamlValue] ≝ {}

covers Sequence ≝ []

documentation Optional ≝ None

download_url Optional[_internal.url.HttpUrl] ≝ None

git_repo Optional[str] ≝ None

icon Union ≝ None

id Optional[DatasetId] ≝ None

id_emoji Optional ≝ None

license Union ≝ None

links Sequence[str] ≝ []

maintainers Sequence ≝ []

maintainers.i.affiliation Optional[str] ≝ None

maintainers.i.email Optional[Email] ≝ None

maintainers.i.orcid Optional ≝ None

maintainers.i.name Optional ≝ None

maintainers.i.github_user str

rdf_source Optional ≝ None

source Optional[_internal.url.HttpUrl] ≝ None

tags Sequence[str] ≝ []

uploader Optional[generic.v0_2.Uploader] ≝ None

uploader.email Email

uploader.name Optional ≝ None

version Optional ≝ None

version_number Optional[int] ≝ None