As part of wider effort towards FAIR data, submissions to the BioImage Archive should feature MIFA-compliant metadata.

If your data requires more information in order to be Findable, Accessible, Interoperable and Reusable, contact us to discuss your use-case.

MifaContainer
publications
Type Publications
Required false
authors
Type List[ Author ]
Required false
grants
Type List[ GrantReference ]
Required false
link_url
Type List[ str ]
Required false
link_description
Type List[ str ]
Required false
title*
Type str
Required true
description*
Type str
Required true
keywords
Type List[ str ]
Required false
license*
Type LicenseType
Required true
ai_models_trained
Type List[ str ]
Required false
acknowledgements
Type str
Required false
funding_statement*
Type str
Required true
annotations*
Type List[ Annotations ]
Required true

Publications

 Information about any publications associated with the dataset
publication_title*
Type str
Required true
publication_authors*
Type str
Required true
publication_doi*
Type str
Required true
publication_year
Type str
Required false
pubmed_id
Type str
Required false

Author

 Information about the authors
organisation
Type List[ OrganisationInfo ]
Required false
author_first_name*
Type str
Required true
author_last_name*
Type str
Required true
email
Type ConstrainedStrValue
Required false
orcid_id
Type str
Required false
role
Type List[ str ]
Required false

OrganisationInfo

 Information about the organisation the author is affiliated with
organisation_name*
Type str
Required true
address
Type str
Required false
ror_id
Type str
Required false

GrantReference

 Information about grant ID and funding body that funded the study
grant_id*
Type str
Required true
funder*
Type str
Required true

LicenseType

 An enumeration.
CC0
Description No Copyright. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
Type Enumeration option
CC_BY
Description You are free to: Share — copy and redistribute the material in any medium or format. Adapt — remix, transform, and build upon the material for any purpose, even commercially. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
Type Enumeration option

Annotations

 A set of annotations for an AI-ready dataset
authors
Type List[ Author ]
Required false
file_metadata
Type List[ FileLevelMetadata ]
Required false
annotation_overview*
Type str
Required true
annotation_type
Type List[ AnnotationType ]
Required false
annotation_method*
Type str
Required true
annotation_criteria
Type str
Required false
annotation_coverage
Type str
Required false
annotation_confidence_level
Type str
Required false

FileLevelMetadata

 metadata atributes that must be detailed at the file level
annotation_id*
Type str
Required true
annotation_type
Type List[ AnnotationType ]
Required false
source_image_id*
Type str
Required true
transformations
Type str
Required false
spatial_information
Type str
Required false
annotation_creation_time
Type datetime
Required false

AnnotationType

 An enumeration.
class_labels
Description tags that identify specific features, patterns or classes in images
Type Enumeration option
bounding_boxes
Description rectangles completely enclosing a structure of interest within an image
Type Enumeration option
counts
Description number of objects, such as cells, found in an image
Type Enumeration option
derived_annotations
Description additional analytical data extracted from the images. For example, the image point spread function,the signal to noise ratio, focus information...
Type Enumeration option
geometrical_annotations
Description polygons and shapes that outline a region of interest in the image. These can be geometrical primitives, 2D polygons, 3D meshes
Type Enumeration option
graphs
Description graphical representations of the morphology, connectivity, or spatial arrangement of biological structures in an image. Graphs, such as skeletons or connectivity diagrams, typically consist of nodes and edges, where nodes represent individual elements or regions and edges represent the connections or interactions between them
Type Enumeration option
point_annotations
Description X, Y, and Z coordinates of a point of interest in an image (for example an object's centroid or landmarks
Type Enumeration option
segmentation_mask
Description an image, the same size as the source image, with the value of each pixel representing some biological identity or background region
Type Enumeration option
tracks
Description annotations marking the movement or trajectory of objects within a sequence of bioimages
Type Enumeration option
weak_annotations
Description rough imprecise annotations that are fast to generate. These annotations are used, for example, to detect an object without providing accurate boundaries
Type Enumeration option
other
Description other types of annotations, please specify in the annotation overview section
Type Enumeration option

    Further information

  • BioImage Archive Online Tutorial

    The BioImage Archive Online Tutorial

  • The BioImage Archive paper

    The BioImage Archive – Building a Home for Life-Sciences Microscopy Data - the paper describing the BioImage Archive Read more

    A call for public archives for biological image data

    A paper detailing the need for the BioImage Archive was featured in Nature Methods in November 2018. Read more

  • Example screening image data

    Examples of bioimages shared and reused. Read more