Published July 27, 2021 | Version 1.7.25-b1 stable beta

Micro-Meta App - Electron implementation

  • 1. Program in Molecular Medicine, UMass Chan 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

Micro-Meta App is an intuitive Graphical User Interface (GUI)-based open-source software that helps scientists to interactively build graphical representations of microscope hardware by dragging-and-dropping individual components onto the workspace and entering the relevant attribute values based on the 4D Nucleome (4DN) - BioImaging North America (BINA) Microscopy Metadata guidelines that scale experimental complexity. From this, Micro-Meta App automatically generates structured Microscope files that can be saved locally, consumed by existing data portals, shared with other scientists, and used repeatedly whenever the same microscope is used to produce image data. Thus, when the image acquisition settings utilized to produce a given image dataset need to be recorded, the user selects the desired image data alongside the relevant Microscope file. Then, Micro-Meta App imports the relevant metadata from the header of image data files to be annotated and interactively guides the user through the collection of all missing attributes. Finally, the App generates a Settings-file, which coupled with the Microscope-file contains comprehensive descriptions of the conditions utilized to produce individual microscopy datasets.

Notes

If you use this software please cite both the software using the metadata indicated below and the papers as indicated in the scope of each reference. 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-Electron-1.7.25-b1.zip

Files (60.2 MB)

Name Size Download all
md5:2b6663656f79e096f91ed6899d091939
60.2 MB Preview Download

Additional details

Funding

National Institutes of Health
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

References

  • Hammer, M., Huisman, M., Rigano, A. et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods 18, 1427–1440 (2021). https://doi.org/10.1038/s41592-021-01327-9
  • Rigano, A., Ehmsen, S., Öztürk, S.U. et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods 18, 1489–1495 (2021). https://doi.org/10.1038/s41592-021-01315-z
  • 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