UMass Chan Medical School Faculty Publications

UMMS Affiliation

RNA Therapeutics Institute; Program in Molecular Medicine

Publication Date


Document Type

Article Preprint


Biochemistry, Biophysics, and Structural Biology | Bioimaging and Biomedical Optics | Bioinformatics | Biotechnology | Data Science | Laboratory and Basic Science Research | Research Methods in Life Sciences


The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America [1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts [4-6].


Imaging, microscopy, metadata, quality control, calibration, standards, data-formats, reproducibility, open microscopy


Huisman M, Hammer M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM. A perspective on Microscopy Metadata: data provenance and quality control. arXiv preprint arXiv:1910.11370. Submitted 2019 Oct 24. Last revised 1 June 2021.


This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.

The PDF available for download is Version 6 of this preprint. The complete version history of this preprint is available at

Earlier versions of this preprint had the title: Minimum information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data.

Full author list omitted for brevity. For the full list of authors, see article.

Journal/Book/Conference Title