Published January 15, 2022 | Version v1-6-19
Dataset Open

Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities

Creators

  • 1. Program in Molecular Medicine, UMass Medical School, Worcester MA 01605, USA
  • 2. Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
  • 3. Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
  • 4. Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
  • 5. Department of Anatomy and Structural Biology, Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461
  • 6. BioCampus Montpellier (BCM), Univ. Montpellier, CNRS, INSERM, Montpellier 34293, France
  • 7. Institut Cochin, Inserm U1016-CNRS UMR8104-Université de Paris, 75014 Paris, France
  • 8. UNC Neuroscience Microscopy Core Facility, Department of Cell Biology & Physiology, Carolina Institute for Developmental Disabilities, & UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599-7250, USA
  • 9. MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
  • 10. Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
  • 11. Center for Cell Imaging, University of Liverpool, Liverpool, L69 3BE, UK
  • 12. Microscopy Resources of the North Quad, University of Harvard Medical School, Boston, MA 02115
  • 13. Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
  • 14. Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
  • 15. Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany

Description

Example Microscopy Metadata (Microscope.JSON and Settings.JSON) files produced using Micro-Meta App to document the Hardware Specifications of example Microscopes and the Image Acquisition Settings utilized to acquire example images as listed in the table below.

For each facility, the dataset contains two JSON files:

  1. Microscope.JSON file (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)
  2. Settings.JSON file (indicated with the name of the image and with the _AS suffix)

Micro-Meta App was developed as part of a global community initiative including the 4D Nucleome (4DN) Imaging Working Group, BioImaging North America (BINA) Quality Control and Data Management Working Group, and QUAlity and REProducibility for Instrument and Images in Light Microscopy (QUAREP-LiMi), to extend the Open Microscopy Environment (OME) data model.

The works of this global community effort resulted in multiple publications featured on a recent Nature Methods FOCUS ISSUE dedicated to Reporting and reproducibility in microscopy.

Learn More! For a thorough description of Micro-Meta App consult our recent Nature Methods and BioRxiv.org publications!

 

Nr. Manufacturer Model Tier Εxperiment Type Facility Name Department and Institution URL References
1 Carl Zeiss Microscopy Axio Observer Z1 (with LSM 710 scan head) 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 Carl Zeiss Microscopy Axio Observer (Axiovert 200M) 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 Carl Zeiss Microscopy Axio Observer Z1 (with Spinning Disk) 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 Carl Zeiss Microscopy Axio Imager Z2 (with Apotome) 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 Carl Zeiss Microscopy Axio Observer Z1 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 Leica Microsystems DMI6000B 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 Leica Microsystems DM5500B 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
  
8 Leica Microsystems DMI8-CS (with TCS SP8 STED 3X) 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 Nikon Instruments Eclipse Ti 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 Nikon Instruments Eclipse Ti-E (HCA) 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 Nikon Instruments/Coleman laboratory (customized) TIRF HILO Epifluorescence light Microscope (THEM)/ Eclipse Ti 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 Nikon Instruments Eclipse Ti (with Andor Dragon Fly Spinning Disk) 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 Nikon Instruments Eclipse Ti2 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 Nikon Instruments Eclipse Ti2 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 Olympus/Biomedical Imaging Group (customized) TIRF Epifluorescence Structured light Microscope (TESM)/IX71 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 Olympus/Computer Vision Laboratory (customized) 3D BrightField Scanner/IX71 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

Getting started

Use these videos to get started with using Micro-Meta App after installation into OMERO and downloading the example data files:

  1. Video 1
  2. Video 2

More information

For full information on how to use Micro-Meta App please utilize the following resources:

  1. Micro-Meta App website
  2. Full documentation
  3. Installation instructions
  4. Step-by-Step Instructions
  5. Tutorial Videos

Background

If you want to learn more about the importance of metadata and quality control to ensure full reproducibility, quality and scientific value in light microscopy, please take a look at our recent publications describing the development of community-driven light 4DN-BINA-OME Microscopy Metadata specifications Nature Methods and BioRxiv.org and our overview manuscript entitled A perspective on Microscopy Metadata: data provenance and quality control.

 

 

Notes

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

Files

01_marcello_pdms_nilered_4nm_subset_nr1_as.json

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Additional details

Funding

4D Nucleome Network Data Coordination and Integration Center 5U01CA200059-03
National Institutes of Health
Visualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imaging 1U01EB021238-01
National Institutes of Health

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, 1427–1440 (2021). https://doi.org/10.1038/s41592-021-01327-9
  • Rigano, A., Ehmsen, S., Öztürk, S.U. et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods 18, 1489–1495 (2021). https://doi.org/10.1038/s41592-021-01315-z