DOI: 10.5281/zenodo.5847476
title: Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities

description: Example <strong>Microscopy Metadata </strong>(Microscope.JSON and Settings.JSON)<strong> files </strong>produced using<strong> Micro-Meta App </strong>to document the <strong>Hardware Specifications</strong> of example Microscopes and the <strong>Image Acquisition Settings</strong> utilized to acquire example images as listed in the table below. For each facility, the dataset contains two JSON files: <strong>Microscope.JSON file</strong> (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json) <strong>Settings.JSON file</strong> (indicated with the name of the image and with the _AS suffix) <strong>Micro-Meta App was</strong> developed as part of a <strong>global community initiative</strong> including the <strong>4D Nucleome (4DN)</strong> Imaging Working Group, <strong>BioImaging North America (BINA)</strong> Quality Control and Data Management Working Group, and <strong>QUAlity and REProducibility for Instrument and Images in Light Microscopy</strong> (<strong>QUAREP-LiMi</strong>), to extend the <strong>Open Microscopy Environment (OME)</strong> data model. The works of this <strong>global community effort</strong> resulted in multiple publications featured on a recent <strong>Nature Methods FOCUS ISSUE </strong>dedicated to Reporting and reproducibility in microscopy. <strong>Learn More!</strong> For a thorough description of <strong>Micro-Meta App</strong> consult our recent Nature Methods and BioRxiv.org publications! <strong>Nr.</strong> <strong>Manufacturer</strong> <strong>Model</strong> <strong>Tier</strong> <strong>Εxperiment Type</strong> <strong>Facility Name</strong> <strong>Department and Institution</strong> <strong>URL</strong> <strong>References</strong> 1 <strong>Carl Zeiss Microscopy</strong> <strong>Axio Observer Z1 (with LSM 710 scan head)</strong> 1 3D visualization of superhydrophobic polymer-nanoparticles Centre for Cell Imaging (CCI) University of Liverpool https://cci.liv.ac.uk/equipment_710.html Upton et al., 2020 2 <strong>Carl Zeiss Microscopy</strong> <strong>Axio Observer (Axiovert 200M)</strong> 2 Μeasurement of illumination stability on Chinese Hamster Ovary cells expressing Paxillin-EGFP Advanced BioImaging Facility (ABIF). McGill University https://www.mcgill.ca/abif/equipment/axiovert-1 Kiepas et al., 2020 3 <strong>Carl Zeiss Microscopy</strong> <strong>Axio Observer Z1 (with Spinning Disk)</strong> 2 Immunofluorescence imaging of cryosection of Mouse kidney Imagerie Cellulaire; Quality Control managed by Miacellavie (https://miacellavie.com/) Centre de recherche du Centre Hospitalier Université de Montréal (CR CHUM), University of Montreal https://www.chumontreal.qc.ca/crchum/plateformes-et-services (the web site is for all core facilities, not specifically for the core facility hosting this microscope) Pilliod et al., 2020 4 <strong>Carl Zeiss Microscopy</strong> <strong>Axio Imager Z2 (with Apotome)</strong> 2 Immunofluorescence imaging of mitotic division in Hela cells using Bioimaging Unit Newcastle University https://www.ncl.ac.uk/bioimaging/ Watson et al., 2020 5 <strong>Carl Zeiss Microscopy</strong> <strong>Axio Observer Z1</strong> 2 Fluorescence microscopy of human skin fibroblasts from Glycogen Storage Disease patients. Life Imaging Center (LIC) Centre for Integrative Signalling Analysis (CISA), University of Freiburg https://miap.eu/equipments/sd-i-abl/ Hannibal et al., 2020 6 <strong>Leica Microsystems</strong> <strong>DMI6000B</strong> 2 3D immunofluorescence imaging rhinovirus infected macrophages IMAG'IC Confocal Microscopy Facility Institut Cochin, CNRS, INSERM, Université de Paris https://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view Jubrail et al., 2020 7 <strong>Leica Microsystems</strong> <strong>DM5500B</strong> 2 Immunofluorescence analysis of the colocalization of PML bodies with DNA double-strand breaks Bioimaging Unit Edwardson Building on the Campus for Ageing and Vitality, Newcastle University https://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview da Silva et al., 2019; Nelson et al., 2012<br> 8 <strong>Leica Microsystems</strong> <strong>DMI8-CS (with TCS SP8 STED 3X)</strong> 2 Live-cell imaging of N. benthamiana leaves cells-derived protoplasts Center for Advanced Imaging (CAi) School of Mathematics/Natural Sciences, Heinrich-Heine-Universität Düsseldorf https://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x Singer et al., 2017; Hänsch et al., 2020 9 <strong>Nikon Instruments</strong> <strong>Eclipse Ti</strong> 2 Immunofluorescence analysis of the cytoskeleton structure in COS cells Advanced Imaging Center (AIC) Janelia Research Campus, Howard Hughes Medical Institute https://www.janelia.org/support-team/light-microscopy/equipment Abdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020 10 <strong>Nikon Instruments</strong> <strong>Eclipse Ti-E (HCA)</strong> 2 Τime-lapse analysis of the bursting behavior of amine-functionalized vesicular assemblies Light Microscopy Facility (IALS-LIF) Institute for Applied Life Sciences, University of Massachusetts at Amherst https://www.umass.edu/ials/light-microscopy Fernandez et al., 2020 11 <strong>Nikon Instruments/Coleman laboratory (customized)</strong> <strong>TIRF HILO Epifluorescence light Microscope (THEM)/ Eclipse Ti</strong> 2 Single-particle tracking of Halo-tagged PCNA in Lox cells Coleman laboratory Anatomy and Structural Biology Department, The Albert Einstein College of Medicine https://einsteinmed.org/faculty/12252/robert-coleman/ Drosopoulos et al., 2020 12 <strong>Nikon Instruments</strong> <strong>Eclipse Ti (with Andor Dragon Fly Spinning Disk)</strong> 2 Investigation of the 3D structure of cerebral organoids Montpellier Resources Imagerie Centre de Recherche de Biologie cellulaire de Montpellier (MRI-CRBM), CNRS, Univerity of Montpellier https://www.mri.cnrs.fr/en/optical-imaging/our-facilities/mri-crbm.html Ayala-Nunez et al., 2019 13 <strong>Nikon Instruments</strong> <strong>Eclipse Ti2</strong> 2 Ιmmunofluorescence imaging of cryosections of mouse hearth myocardium Neuroscience Center Microscopy Core Neuroscience Center, University of North Carolina https://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/ Aghajanian et al., 2021 14 <strong>Nikon Instruments</strong> <strong>Eclipse Ti2</strong> 2 Live-cell imaging of bacterial cells expressing GFP-PopZ Microscopy Resources on the North Quad (MicRoN) Harvard Medical School https://micron.hms.harvard.edu/ Lim and Bernhardt 2019; Lim et al., 2019 15 <strong>Olympus/Biomedical Imaging Group (customized)</strong> <strong>TIRF Epifluorescence Structured light Microscope (TESM)/IX71</strong> 3 3D distribution of HIV-1 in the nucleus of human cells Biomedical Imaging Group Program in Molecular Medicine, University of Massachusetts Medical School https://trello.com/b/BQ8zCcQC/tirf-epi-fluorescence-structured-light-microscope Navaroli et al., 2012 16 <strong>Olympus/Computer Vision Laboratory (customized)</strong> <strong>3D BrightField Scanner/IX71</strong> 3 Transmitted light brightfield visualization of swimming spermatocytes Laboratorio Nacional de Microscopia Avanzada (LNMA) and Computer Vision Laboratory of the Institute of Biotechnology Universidad Nacional Autonoma de Mexico (UNAM) https://lnma.unam.mx/wp/ Pimentel et al., 2012; Silva-Villalobos et al., 2014 <strong>Getting started</strong> Use these videos to get started with using Micro-Meta App after installation into OMERO and downloading the example data files: Video 1 Video 2 <strong>More information</strong> For full information on how to use Micro-Meta App please utilize the following resources: Micro-Meta App website Full documentation Installation instructions Step-by-Step Instructions Tutorial Videos <strong>Background</strong> If you want to learn more about the importance of <strong>metadata and quality contro</strong>l to ensure full <strong>reproducibility, quality and scientific value</strong> in light microscopy, please take a look at our recent publications describing the development of community-driven light <strong>4DN-BINA-OME Microscopy Metadata</strong> specifications Nature Methods and BioRxiv.org and our overview manuscript entitled <strong>A perspective on Microscopy Metadata: data provenance and quality control</strong>.
description: Additional support: -- NSF grant #1917206 to D.G.; -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant #2019-198155 (5022) awarded to C.S.D.C. as part of the Imaging Scientist Program. -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant ##2020-225398 awarded to C.M.B. as part of the Imaging Scientist Program
description: {"references": ["Rigano A, Ehmsen S, Ozturk SU, Ryan J, Balashov A, Hammer M, et al. Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications. BioRxiv [Internet]. 2021; Available from: https://www.biorxiv.org/content/10.1101/2021.05.31.446382v1", "Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. BioRxiv [Internet]. 2021 Apr 25; Available from: https://www.biorxiv.org/content/10.1101/2021.04.25.441198v1", "Huisman M, Hammer M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, et al. A perspective on Microscopy Metadata: data provenance and quality control [Internet]. arXiv [q-bio.QM]. 2021. Available from: https://arxiv.org/abs/1910.11370", "1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: 1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: https://vimeo.com/562022222", "1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: 1/2 Instructional video on how to use these example data files to get started with Micro-Meta App. Available at: https://vimeo.com/562022281", "Hammer, M., Huisman, M., Rigano, A. et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods 18, 1427\u20131440 (2021). https://doi.org/10.1038/s41592-021-01327-9", "Rigano, A., Ehmsen, S., \u00d6zt\u00fcrk, S.U. et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods 18, 1489\u20131495 (2021). https://doi.org/10.1038/s41592-021-01315-z"]}