MISFISHIE Standard Working Group

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Welcome to the website of the MISFISHIE Standard Working Group for the MGED project. This working group has been set up to develop and promote the MISFISHIE standard as a community effort.


MISFISHIE is the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments. This specification details the minimum information that should be provided when publishing, making public, or exchanging results from visual interpretation-based tissue gene expression localization experiments such as in situ hybridization, immunohistochemistry, reporter construct genetic experiments (GFP/green fluorescent protein, β-galactosidase), etc. Compliance to this standard is expected to provide researchers at other labs enough information to reproduce the experiment and/or to fully evaluate the data upon which results are based.


Modeled after the well-received MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments, this specification only describes the types of information that should be provided. This specification does not dictate a specific format for reporting the information. We expect to develop a data model based on the concepts of MAGE-OM (MicroArray Gene Expression Object Model) and on the MAGEstk (MicroArray Gene Expression software tool kit) in the near future. It is this model and the associated XML-based markup language that will provide the recommended data format for archiving or transferring such data. Separation of the minimum information specification and the data format is important because the data format should both allow for unlimited additional information as well as some degree of partial information for optimum usefulness.

The specification describes the type of information that must be provided in six sections:

  1. Experimental Design
  2. Specimens
  3. Probe or Antibody Information
  4. Staining Protocols and Parameters
  5. Imaging Data and Parameters
  6. Image Characterization

The primary imaging data is a requirement since the interpretation of in situ or immunohistochemistry images is subject to observer variability. Furthermore, many specimens are unique; consequently, exact reproduction can be problematic or impossible. The final section provides a basic system for describing the interpretation of the images in a way that can be searched and collated in an automated fashion.

The Specification:

The full MISFISHIE standard is here.


This specification was jointly developed by members of the NIH/NIDDK Stem Cell Genome Anatomy Projects consortium in order to facilitate data sharing within the consortium. After successfully serving the consortium, it is being proposed to the whole research community by the MGED Society.

Ontology presentations:

  • [PPT] [PDF]: Presentation at SOFG2 -- Standards and Ontologies for Functional Genomics (Philadelphia, PA, USA - November, 2004)


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Please contact Eric Deutsch with questions, comments or requests about this site or the working group.

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