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Nature Methods > Focus Issue

Reporting and reproducibility in microscopy

This Focus issue features a series of papers offering guidelines and tools for improving the tracking and reporting of microscopy metadata with an emphasis on reproducibility and data re-use.

Citation: Reporting and reproducibility in microscopy. Nature Methods 18 (12), (2021).

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Data Management and Sharing

Bajcsy, P. et al. Enabling global image data sharing in the life sciences - peer reviewed. Nat. Methods 22, 672–676 (2025). DOI: 10.1038/s41592-024-02585-z

Bialy, N. et al. Harmonizing the generation and pre-publication stewardship of FAIR image data. ArXiv (2024). DOI: 10.48550/arXiv.2401.13022

Community Building

Reis, Y. et al. People-Centred Funding as a Catalyst for Sustainable Imaging Infrastructure. J. Microsc. (2024). DOI: 10.1111/jmi.70099

De Niz, M. et al. Building momentum through networks: Bioimaging across the Americas. J. Microsc. 294(special issue), 420–439 (2024). DOI: 10.1111/jmi.13318

Community Guidelines

Montero Llopis, P. et al. Better Reporting is Better Science: Community-Defined Minimal Reporting Requirements for Light Microscopy. J. Cell Biol. 225, e202601032 (2026). DOI: 10.1083/jcb.202601032

Cimini, B. A. et al. The crucial role of bioimage analysts in scientific research and publication. J. Cell Sci. 137, jcs262322 (2024). DOI: 10.1242/jcs.262322

Schmied, C. et al. Community-developed checklists for publishing images and image analyses. Nat. Methods 21 (2023). DOI: 10.1038/s41592-023-01987-9

Data and Metadata Standards

Moxon, S. A. T. et al. LinkML: an open data modeling framework. Gigascience 15 (2026). DOI: 10.1093/gigascience/giad113

Moore, J. et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem. Cell Biol. (2023). DOI: 10.1007/s00418-023-02209-1

FAIR Facilities and Instruments

Mayernik, M. et al. Recommendations Toward a Framework for Adoption and Use of Persistent Identifiers for Research Facilities, Platforms, and Instruments. Zenodo (2026). DOI: 10.5281/zenodo.18436644

Mayernik, M. et al. FAIR Facilities and Instruments Workshop #3 Report: Synthesizing Community Input Toward Recommendations. University of Colorado Boulder (2026). DOI: 10.25810/QYD9-2T28

Research Resource Identification (RRID)

Bandrowski, A. A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?. Gigascience 11 (2022). DOI: 10.1093/gigascience/giac058