ArticleNature methods2021
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.
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Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers, 1 of them a synthesis that pooled it.
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25citing papers in PubMed, 1 pooled it
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Bridging imaging-based in vitro methods from biomedical research to regulatory toxicology.Archives of toxicology · 2025Review
- MetaMax: an objective-sized instrument for advanced light microscope characterization and performance metadata collection.Optics express · 2025Article
- High-throughput image processing software for the study of nuclear architecture and gene expression.Scientific reports · 2024Article
- Super-enhancer interactomes from single cells link clustering and transcription.bioRxiv : the preprint server for biology · 2024Article
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- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Molecular cell · 2023Review
- Loop stacking organizes genome folding from TADs to chromosomes.Molecular cell · 2023Article
- Elucidating the structure and function of the nucleus-The NIH Common Fund 4D Nucleome program.Molecular cell · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
33 authors.
Alessandro RiganoProgram in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.
Shannon EhmsenDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Serkan Utku ÖztürkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Joel RyanAdvanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.ORCID http://orcid.org/0000-0002-7295-815X
Alexander BalashovDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Mathias HammerRNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
Koray KirliDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Ulrike BoehmJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0001-7471-2244
Claire M BrownAdvanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.ORCID http://orcid.org/0000-0003-1622-663X
Karl BellveProgram in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0003-3889-468X
James J ChambersInstitute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
Andrea CosoloDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3417-0713
Robert A ColemanDepartment of Anatomy and Structural Biology, Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
Orestis FaklarisBioCampus Montpellier (BCM), University of Montpellier, CNRS, INSERM, Montpellier, France.ORCID http://orcid.org/0000-0001-5965-5405
Kevin E FogartyProgram in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.
Thomas GuilbertInstitut Cochin, Inserm U1016-CNRS UMR8104-Université de Paris, Paris, France.ORCID http://orcid.org/0000-0001-5069-0730
Anna B HamacherCenter for Advanced Imaging, Heinrich-Heine University Duesseldorf, Düsseldorf, Germany.
Michelle S ItanoUNC 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.ORCID http://orcid.org/0000-0001-6853-1228
Daniel P KeeleyUNC 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.
Susanne KunisDepartment of Biology/Chemistry and Center for Cellular Nanoanalytics, University Osnabrück, Osnabrück, Germany.ORCID http://orcid.org/0000-0001-6523-7496
Judith LacosteMIA Cellavie Inc., Montreal, Quebec, Canada.ORCID http://orcid.org/0000-0002-8783-8599
Alex LaudeBioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.
Willa Y MaUNC Neuroscience Microscopy Core Facility, Carolina Institute for Developmental Disabilities, and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
Marco MarcelloCenter for Cell Imaging, University of Liverpool, Liverpool, UK.ORCID http://orcid.org/0000-0002-2392-8640
Paula Montero-LlopisMicroscopy Resources of the North Quad, University of Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-5983-2296
Glyn NelsonBioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-1895-4772
Roland NitschkeLife Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-9397-8475
Jaime A PimentelLaboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.ORCID http://orcid.org/0000-0001-8569-0466
Stefanie Weidtkamp-PetersCenter for Advanced Imaging, Heinrich-Heine University Duesseldorf, Düsseldorf, Germany.ORCID http://orcid.org/0000-0001-7734-3771
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-9378-960X
Burak H AlverDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
David GrunwaldRNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0001-9067-804X
Caterina Strambio-De-CastilliaProgram in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA. caterina.strambio@umassmed.edu.ORCID http://orcid.org/0000-0002-1069-1816
Funding
4D Nucleome Network Data Coordination and Integration CenterU01CA200059 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2024
$24.4MUNC Neuroscience Center Research Cores: MicroscopyP30NS045892 · NINDS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI ZYLKA, MARK J. · 2003 to 2022
$11.5MPreclinical CoreP50HD103573 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI GABRIEL S DICHTER · 2020 to 2026
$9.7MSUPPORT FOR THE ROSE F KENNEDY IDDRC P50P50HD105352 · NICHD · ALBERT EINSTEIN COLLEGE OF MEDICINE · PI SOPHIE MOLHOLM, Steven Upshaw Walkley · 2021 to 2026
$7.0MDissecting the Dynamic Interplay Between, p53, Chromatin and Transcriptional Bursting in Single CellsR01GM126045 · NIGMS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI COLEMAN, ROBERT · 2018 to 2025
$2.9MVisualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imagingU01DA047733 · NIDA · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GRUNWALD, DAVID · 2018 to 2019
$1.0MVisualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imagingU01EB021238 · NIBIB · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GRUNWALD, DAVID · 2015 to 2017
$990kNCI NIH HHS U01 CA200059NIBIB NIH HHS U01 EB021238NICHD NIH HHS P50 HD103573NICHD NIH HHS P50 HD105352NIDA NIH HHS U01 DA047733NIGMS NIH HHS R01 GM126045NINDS NIH HHS P30 NS045892
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.
Indexed as
MetadataMobile ApplicationsProgramming LanguagesSoftwareAnimalsCell LineComputational BiologyHumansImage Processing, Computer-AssistedMiceMicroscopy, ConfocalMicroscopy, FluorescencePattern Recognition, AutomatedQuality ControlReproducibility of ResultsUser-Computer Interface
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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.