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

Nat Methods. 2021 Dec;18(12):1489-1495. doi: 10.1038/s41592-021-01315-z. Epub 2021 Dec 3.

Authors

Alessandro Rigano¹, Shannon Ehmsen², Serkan Utku Öztürk², Joel Ryan³, Alexander Balashov², Mathias Hammer⁴, Koray Kirli², Ulrike Boehm⁵, Claire M Brown³, Karl Bellve¹, James J Chambers⁶, Andrea Cosolo², Robert A Coleman⁷, Orestis Faklaris⁸, Kevin E Fogarty¹, Thomas Guilbert⁹, Anna B Hamacher¹⁰, Michelle S Itano¹¹, Daniel P Keeley¹¹, Susanne Kunis¹², Judith Lacoste¹³, Alex Laude¹⁴, Willa Y Ma¹⁵, Marco Marcello¹⁶, Paula Montero-Llopis¹⁷, Glyn Nelson¹⁴, Roland Nitschke¹⁸, Jaime A Pimentel¹⁹, Stefanie Weidtkamp-Peters¹⁰, Peter J Park², Burak H Alver², David Grunwald⁴, Caterina Strambio-De-Castillia²⁰

Affiliations

¹ Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.
² Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
³ Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.
⁴ RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
⁵ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
⁶ Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
⁷ Department of Anatomy and Structural Biology, Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
⁸ BioCampus Montpellier (BCM), University of Montpellier, CNRS, INSERM, Montpellier, France.
⁹ Institut Cochin, Inserm U1016-CNRS UMR8104-Université de Paris, Paris, France.
¹⁰ Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, Düsseldorf, Germany.
¹¹ UNC Neuroscience Microscopy Core Facility, Department of Cell Biology and Physiology, Carolina Institute for Developmental Disabilities, and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
¹² Department of Biology/Chemistry and Center for Cellular Nanoanalytics, University Osnabrück, Osnabrück, Germany.
¹³ MIA Cellavie Inc., Montreal, Quebec, Canada.
¹⁴ Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.
¹⁵ UNC Neuroscience Microscopy Core Facility, Carolina Institute for Developmental Disabilities, and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
¹⁶ Center for Cell Imaging, University of Liverpool, Liverpool, UK.
¹⁷ Microscopy Resources of the North Quad, University of Harvard Medical School, Boston, MA, USA.
¹⁸ Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany.
¹⁹ Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
²⁰ Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA. [email protected].

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Cell Line
Computational Biology / methods
Humans
Image Processing, Computer-Assisted
Metadata*
Mice
Microscopy, Confocal / instrumentation*
Microscopy, Confocal / methods*
Microscopy, Fluorescence / instrumentation*
Microscopy, Fluorescence / methods*
Mobile Applications*
Pattern Recognition, Automated
Programming Languages*
Quality Control
Reproducibility of Results
Software*
User-Computer Interface
Workflow

Abstract

Publication types

MeSH terms

Grants and funding