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Published May 12, 2021 | Version 0.0.0.20b7
Software Open

WU-BIMAC/MicroMetaApp-React: 1.2.2-b1-1 stable beta (4DN v5 Integration - VII)

Creators

  • 1. Program in Molecular Medicine, UMass Medical School, Worcester MA 01605, USA
  • 2. Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
  • 3. Karya SMD + Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA

Description

This is the latest stable beta release of the React implementation of the Micro-Meta App.

This version of the Micro-Meta App is based on the Core and Basic extension of the v2.01 of the 4DN-BINA-OME Microscopy Metadata specifications which allow documenting transmitted light, epifluorescence, structured-light, and TIRF light microscopy. With Micro-Meta App you can:

1) Use the Manage Instrument component of the App to document the hardware configuration of a specific Microscope and produce a structured Microscop JSON file containing Hardware Specifications metadata.

2) Use the Manage Settings component of the App to document the Image Acquisition Settings that were used to collect a specific image dataset. In this section, the App imports Hardware Specifications metadata from a previously created Microscoe.json file, uses Bio-Formats to import available Microscopy Metadata from the file header of an image produced using the selected Microscope, collects missing Image Acquisition Settings, and saves the resulting Image Acquisition Settings metadata in a specific Settings.json file.

Full instructions on how to use the App are available here

The source code is available as follows:

-Javascript React implementation is available here

-Javascript Electron-wrapped implementation is available here

-Prototype OMERO plugin is available here

Notes

Additional support: -- NSF grant #1917206 to D.G.; -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant #2019-198155 (5022) awarded to C.S.D.C. as part of the Imaging Scientist Program. -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant ##2020-225398 awarded to C.M.B. as part of the Imaging Scientist Program. - Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant number Ni 451/9-1 MIAP-Freiburg, to R.N.

Files

WU-BIMAC/MicroMetaApp-React-0.0.0.20b7.zip

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Additional details

Related works

Is supplement to
https://github.com/WU-BIMAC/MicroMetaApp-React/tree/0.0.0.20b7 (URL)

Funding

4D Nucleome Network Data Coordination and Integration Center 5U01CA200059-03
National Institutes of Health
Visualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imaging 1U01EB021238-01
National Institutes of Health

References

  • Huisman M, Hammer M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, et al. A perspective on Microscopy Metadata: data provenance and quality control [Internet]. arXiv [q-bio.QM]. 2021. Available from: https://arxiv.org/abs/1910.11370
  • Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. BioRxiv [Internet]. 2021 Apr 25; Available from: https://www.biorxiv.org/content/10.1101/2021.04.25.441198v2