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

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:

Microscope.JSON file (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)

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:

Video 1

Video 2

More information

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

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.