[ome-devel] Proposal for 4D Nucleome Microscopy Metadata Guidelines based on the OME data model

[Strambio, Caterina]

Dear All

the 4D Nucleome Imaging Standards Working Group would like to solicit feedback on proposed guidelines we are putting forwards for a metadata standard for describing:

1) MICROSCOPE HARDWARE Specifications
2) IMAGE ACQUISITION Settings
3) OPTICAL, FIELD, EXCITATION POWER and WAVELENGTH, and DETECTOR CALIBRATION Procedures

used to document imaging experiments and foster their reproducibility.

The guidelines incorporate and update the OME data model and aim at increasing data fidelity, easing future analysis and facilitating objective comparison of different imaging datasets and imaging experiments setups.

The proposed 4DN-OME guidelines have the following distinctive features:

1) Based on the premise that not all imaging experiments are “created equal” and that different reporting guidelines might be required depending upon the experimental intent, we propose a Tiered system of  guidelines that specify what kind of metadata is required for different kind of imaging experiments.

2) Attempt to transition the OME data model towards a clear set of community standards that could serve as a basis for an “Encode”-like standard for imaging.

3) Help to guide different stake holders, including manufacturers, experimental and computational biologists, peer reviewers, publishers and funding agencies in evaluating of the performance,  quality and uncertainty associated with specific microscope setups.

The current version of the metadata model and tier system description can be found on GitHub at the following address:

https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines

Please feel free to contact us for any question, concern, comment, (constructive) criticism.

Cheers

Caterina Strambio De Castillia and David Grunwald


----------------
Caterina Strambio De Castillia, Ph.D. | Chan Zuckerberg Initiative Imaging Scientist |
Assistant Professor, Program in Molecular Medicine |
The University of Massachusetts Medical School | 373 Plantation Street, Biotech II, Suite 114
Worcester, MA 01605, USA |
+ 1 857-288-9331 | caterina.strambio at umassmed.edu<mailto:caterina.strambio at umassmed.edu> | http://big.umassmed.edu/omegaweb/ | @StrambioLab







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