Cell Biology

Standards Add

ISA-Tab Edit

The Investigation/Study/Assay (ISA) tab-delimited (TAB) format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from 'omics-based' experiments employing a combination of technologies.

Created by core developers from the University of Oxford, ISA-TAB v1.0 was released in November 2008.

MIBBI (Minimum Information for Biological and Biomedical Investigations) Edit

A common portal to a group of nearly 40 checklists of Minimum Information for various biological disciplines. The MIBBI Foundry is developing a cross-analysis of these guidelines to create an intercompatible, extensible community of standards.

The concept was realized initially through the joint efforts of the Proteomics Standards Initiative, the Genomic Standards Consortium and the MGED RSBI Working Groups. The latest project to register with MIBBI is the MIABie guidelines for reporting biofilm research, as of January 2012.

OME-XML (Open Microscopy Environment XML) Edit

OME-XML is a vendor-neutral file format for biological image data, with an emphasis on metadata supporting light microscopy. It can be used as a data file format in its own right, or as a way of encoding metadata within a TIFF or BigTIFF file (for which purpose there is the OME-TIFF specification).

The standard is maintained by the Open Microscopy Environment Consortium, and was last updated in June 2012.

Extensions Add

OME-TIFF (Open Microscopy Environment TIFF) Edit

A specification of how to embed OME-XML metadata within a TIFF or BigTIFF image file.


An ISA-Tab-based standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments.

Tools Add

Bio-Formats Edit

Bio-Formats reads proprietary microscopy image data and metadata, and converts them to OME-TIFF, a combination of TIFF and OME-XML.

Fiji Edit

Fiji is an image processing package that supports the OME data model for images

ISA Software Suite Edit

The open source ISA metadata tracking tools facilitate ISA-TAB-compliant collection, curation, local management and reuse of datasets in an increasingly diverse set of life science domains.


Repository software for organising, viewing, analysing and sharing biological microscopy images. It supports proprietary file formats but normalises to OME-TIFF/OME-XML.

Use Cases Add

The Cell: An Image Library Edit

A resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. Its native metadata format for images is OME-XML.

FlowRepository Edit

A database of flow cytometry experiments where you can query and download data collected and annotated according to the MIBBI-registered MIFlowCyt standard.

Harvard Medical School LINCS Database Edit

One of two research centers in the US creating libraries of signatures that describe how cells respond to perturbation, it uses the ISA-TAB standard to describe its data.

ISA Commons Edit

A network of systems and projects that use the ISA-Tab file format, and/or are powered by components of the ISA software suite.

JCB Data Viewer Edit

A repository for viewing and analysing multi-dimensional image data associated with articles published in The Journal of Cell Biology. Its native metadata format is OME-XML.