Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Alessandro Rigano; Shannon Ehmsen; Serkan Utku Öztürk; Joel Ryan; Alexander Balashov; Mathias Hammer; Koray Kirli; Ulrike Boehm; Claire M. Brown; Karl Bellve; James J. Chambers; Andrea Cosolo; Robert A. Coleman; Orestis Faklaris; Kevin E. Fogarty; Thomas Guilbert; Anna B. Hamacher; Michelle S. Itano; Daniel P. Keeley; Susanne Kunis; Judith Lacoste; Alex Laude; Willa Y. Ma; Marco Marcello; Paula Montero-Llopis; Glyn Nelson; Roland Nitschke; Jaime A. Pimentel; Stefanie Weidtkamp-Peters; Peter J. Park; Burak H. Alver; David Grunwald; Caterina Strambio-De-Castillia

doi:10.1038/s41592-021-01315-z

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Alessandro Rigano, Shannon Ehmsen, Serkan Utku Öztürk, Joel Ryan, Alexander Balashov, Mathias Hammer, Koray Kirli, Ulrike Boehm, Claire M. Brown, Karl Bellve, James J. Chambers, Andrea Cosolo, Robert A. Coleman, Orestis Faklaris, Kevin E. Fogarty, Thomas Guilbert, Anna B. Hamacher, Michelle S. Itano, Daniel P. Keeley, Susanne KunisJudith Lacoste, Alex Laude, Willa Y. Ma, Marco Marcello, Paula Montero-Llopis, Glyn Nelson, Roland Nitschke, Jaime A. Pimentel, Stefanie Weidtkamp-Peters, Peter J. Park, Burak H. Alver, David Grunwald, Caterina Strambio-De-Castillia

Cell Biology

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.

Original language	English (US)
Pages (from-to)	1489-1495
Number of pages	7
Journal	Nature Methods
Volume	18
Issue number	12
DOIs	https://doi.org/10.1038/s41592-021-01315-z
State	Published - Dec 2021

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Rigano, A., Ehmsen, S., Öztürk, S. U., Ryan, J., Balashov, A., Hammer, M., Kirli, K., Boehm, U., Brown, C. M., Bellve, K., Chambers, J. J., Cosolo, A., Coleman, R. A., Faklaris, O., Fogarty, K. E., Guilbert, T., Hamacher, A. B., Itano, M. S., Keeley, D. P., ... Strambio-De-Castillia, C. (2021). Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nature Methods, 18(12), 1489-1495. https://doi.org/10.1038/s41592-021-01315-z

Rigano, A, Ehmsen, S, Öztürk, SU, Ryan, J, Balashov, A, Hammer, M, Kirli, K, Boehm, U, Brown, CM, Bellve, K, Chambers, JJ, Cosolo, A, Coleman, RA, Faklaris, O, Fogarty, KE, Guilbert, T, Hamacher, AB, Itano, MS, Keeley, DP, Kunis, S, Lacoste, J, Laude, A, Ma, WY, Marcello, M, Montero-Llopis, P, Nelson, G, Nitschke, R, Pimentel, JA, Weidtkamp-Peters, S, Park, PJ, Alver, BH, Grunwald, D & Strambio-De-Castillia, C 2021, 'Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications', Nature Methods, vol. 18, no. 12, pp. 1489-1495. https://doi.org/10.1038/s41592-021-01315-z

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abstract = "For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.",

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AU - Kirli, Koray

AU - Boehm, Ulrike

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AU - Bellve, Karl

AU - Chambers, James J.

AU - Cosolo, Andrea

AU - Coleman, Robert A.

AU - Faklaris, Orestis

AU - Fogarty, Kevin E.

AU - Guilbert, Thomas

AU - Hamacher, Anna B.

AU - Itano, Michelle S.

AU - Keeley, Daniel P.

AU - Kunis, Susanne

AU - Lacoste, Judith

AU - Laude, Alex

AU - Ma, Willa Y.

AU - Marcello, Marco

AU - Montero-Llopis, Paula

AU - Nelson, Glyn

AU - Nitschke, Roland

AU - Pimentel, Jaime A.

AU - Weidtkamp-Peters, Stefanie

AU - Park, Peter J.

AU - Alver, Burak H.

AU - Grunwald, David

AU - Strambio-De-Castillia, Caterina

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Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Abstract

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