WG 7 - Objectives
The Work Group 7 focuses on various aspects of Image Metadata (initially primarily Microscopy Metadata but also Sample and Analysis Metadata). These span from defining and continually revising the 4DN-BINA-OME (NBO) Microscopy Metadata model, to facilitating metadata capture through user-friendly tools, to integrating the captured metadata into cloud-ready storage containers such as the newly developed Open Microscopy Environment (OME) Next-Generation File Format (NGFF). To promote the uptake of metadata tools and models, educational material and outreach strategies are also developed.
To carry on these tasks, WG7 is organized into four Subgroups (see “Subgroup” tab below), each of which carries out specific objectives. These subgroups are created, paused, or dissolved on a needs basis as agreed by the WG7 as a whole.
The general meeting serves as a space for reporting back on the progress that has been achieved within the Subgroups, connecting the dots, strategic planning, and general discussions.
The Subgroups (see “Subgroup” tab below) identify specific tasks to be carried out to move our work forward. To participate, please first fill in the general QUAREP-LiMi membership form and then enter your name here. Still confused? No worries, we have a specific list of tasks that you can check out to know exactly how you can lend a hand.
WG 7 - Co-Chairs
Josh Moore
WG 7 - Latest News
We welcome our first member from the United Arab Emirates. Rachid Rezgui of NYU Abu Dhabi joined the Working Groups 1-7, 9, 10 and 13. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.
We welcome our first member from the China. Xiaoming Li from ShanghaiTech University, joined the Working Groups 1 to 11. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.
Last meeting: 8th July 2024, 4:00 pm
Global Bioimaging Training Module: Reporting and Reproducibility in Microscopy.
- Reporting and Reproducibility in Microscopy modules are dedicated to image metadata, an essential additional information including dimensions, pixel size, image type, bit depth, and microscope settings, all necessary for extraction of meaningful data from images, quantitative image analysis, and reproducibility of experiments. The training module can be found here.
Protocols.io: Getting started with Micro-Meta App Tutorial
- The tutorial can be found here.
NBO Microscopy Metadata Specifications (full name 4DN–BINA-OME):
- Hammer, Mathias, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Alison J. North, et al. “Towards Community-Driven Metadata Standards for Light Microscopy: Tiered Specifications Extending the OME Model.” Nature Methods, December 3, 2021, 1–14. https://doi.org/10.1038/s41592-021-01327-9. CITE
- Huisman, Maximiliaan, et al. “A perspective on Microscopy Metadata: data provenance and quality control.” arXiv, 24 Oct. 2019, arxiv.org/abs/1910.11370v6.
- Explore
- Provide feedback (How to)
Micro-Meta-App
- Rigano, Alessandro, Shannon Ehmsen, Serkan Utku Öztürk, Joel Ryan, Alexander Balashov, Mathias Hammer, Koray Kirli, et al. “Micro-Meta App: An Interactive Tool for Collecting Microscopy Metadata Based on Community Specifications.” Nature Methods, December 3, 2021, 1–7. https://doi.org/10.1038/s41592-021-01315-z. CITE
- Download
- How to
- Provide feedback
MethodsJ2
- Ryan, Joel, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, and Claire M. Brown. “MethodsJ2: A Software Tool to Capture Metadata and Generate Comprehensive Microscopy Methods Text.” Nature Methods, October 15, 2021, 1–3. https://doi.org/10.1038/s41592-021-01290-5. CITE
- Download
- How to
MDEmic (OMERO.mde implementation)
- Kunis, Susanne, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, and Stefanie Weidtkamp-Peters. “MDEmic: A Metadata Annotation Tool to Facilitate Management of FAIR Image Data in the Bioimaging Community.” Nature Methods, October 11, 2021, 1–2. https://doi.org/10.1038/s41592-021-01288-z. CITE
- Download
- How to
- GitHub
- Subgroup: Improving the usability of Metadata tools
- Aims: Develop user-friendly tools to input, update, and visualize image metadata.
- Co-leads: Caterina Strambio De Castillia and Roland Nitschke
- Contact information: caterina.strambio@umassmed.edu
- On-going tasks:
- Provide feedback for the design and usability of Micro-Meta App canvases for capturing Laser Scanning Confocal (LSM) and for Spinning Disk Confocal (SDC)
- Cloud storage location (can be accessed as a member) → here
- Subgroup: Metadata education and outreach
- Aims: Develop guidelines and educational material for users to understand and record image metadata
- Co-leads: Nathalie Gaudreault and Aastha Mathur
- Contact information: aastha.mathur@eurobioimaging.eu
- Cloud storage location (can be accessed as a member) → here
- Subgroup: Metadata storage specifications
- Aims: Develop ways and options (e.g., OMERO) to store/manage/retrieve metadata together with image data and, in particular, OME-NGFF
- Co-leads: Guillaume Gay, Ken Ho, and Damir Sudar
- Contact information: dsudar@qitissue.comandkenneth.ho@crick.ac.uk
- On-going tasks:
- Developing Micro-Meta App plugin for OMERO.web
- Integrating Micro-Meta App with OMERO.mde
- OWL/RDF ontology
- Testing JSON-LD as a standard for metadata storage for OME-NGFF
- Cloud storage location (can be accessed as a member) → here
- Subgroup: Metadata model revision
- Aims: Revise the published version of the 4DN-BINA-OME Microscopy Metadata on the basis of feedback from commercial manufacturers and the imaging community.
- Lead: Caterina Strambio De Castillia
- Contact information: caterina.strambio@umassmed.edu
- On-going tasks:
- Implement changes requested for the Detector/Camera model collected during a series of meetings held in Spring 2022 with Camera manufacturers and organized jointly by WG2 and WG7
- Cloud storage location (can be accessed as a member) → here
Memberlist WG 7
Last name First Name Town Organisation Affiliation Lab Affiliation Country Time Zone
Acton
Richard
Cambridge
Human Developmental Biology Initiative
Univ.
GB
UTC+-0
Alshafie
Walaa
Ashburn
Janelia research campus
Univ.
US
UTC-4
Asmar
Anthony
Gaithersburg
National Institute of Standards and Technology
Gov.
US
UTC-4
Bagley
Steve
Manchester
University of Manch.
Univ.
GB
UTC+1
Bain
Virginia
Danvers
Cell Signaling Technology
Industry
US
UTC-5
Banerjee
Priyam
New York
Rockefeller University
Univ.
US
UTC-5
Bassi
Andrea
Milano
Politecnico di Milano
Univ.
IT
UTC+2
Beavers
Nick
Rockville
Media Cybernetics
Industry
US
UTC-4
Beckert
Hannes
Bonn
GerBi-GMB WG 1
Univ.
DE
UTC+2
Belyaev
Ivan
Jena
Friedrich Schiller University Jena
Univ.
DE
UTC+2
Biehlmaier
Oliver
Basel
Imaging Core Facility, Biozentrum, Basel
Univ.
CH
UTC+1
Blazikova
Michaela
Prague
Light Microscopy Core Facility, IMG CAS
Univ.
CZ
UTC+1
Boehm
Ulrike
Oberkochen
Carl Zeiss AG
Industry
DE
UTC-4
Bourg
Nicolas
Cachan
Abbelight
Industry
FR
UTC+1
Bourn
Matthew
Leeds
National Measurement Laboratory
Industry
GB
UTC+1
Breitlow
Juergen
Berlin
PicoQuant GmbH
Industry
DE
UTC+1
Budde
Kai
Rostock
University of Rostock
Univ.
DE
UTC+2
Capek
Martin
Prague
Institute of Molecular Genetics of the Czech Academy of Sciences
Gov.
CZ
UTC+1
Carvalho
Mariana
Braga
INL – International Iberian Nanotechnology Laboratory
EU-Org
PT
UTC+-0
Casas-Moreno
Xavier
Solna
KTH Royal Institute of Technology
Univ.
SE
UTC+1
Cebecauer
Marek
Prague
J. Heyrovsky Institute of Physical Chemistry
Gov.
CZ
UTC+1
Chacko
Jenu
Madison
University of Wisconsin-Madison
Univ.
US
UTC-6
Chambers
James
Boston
BINA
Univ.
US
UTC-4
Chen
Lily
Hayward
Eikon Therapeutics
Industry
US
UTC-8
Chinnaraj
Subash Bommu
Amstelveen
Nikon Europe B.V.
Industry
NL
UTC+1
Cimini
Beth
Cambridge
Broad Institute
Univ.
US
UTC-4
Cole
Louise
Sydney
University of Technology
Univ.
AU
UTC+11
Conde-Sousa
Eduardo
Porto
INEB/i3S
Univ.
PT
UTC+0
Condon
Nicholas
Brisbane
University of Queensland
Univ.
AU
UTC+10
Contremoulins
Vincent
Paris
CNRS
Univ.
FR
UTC+2
De Niz
Mariana
Chicago
Northwestern University
Univ.
US
UTC-5
Dhmine
Oumou
Monpellier
CNRS
Gov.
FR
UTC+1
Diez-Guerra
F. Javier
Madrid
CBMSO (CSIC-UAM)
Univ.
ES
UTC+2
Dobbie
Ian
Baltimore
Johns Hopkins University
Univ.
US
UTC+5
Duong
Cao Nguyen
Saarbrücken
Leibniz Institute for New Materials
Leibniz
DE
UTC+1
Ecker
Rupert
Vienna
TissueGnostics GmbH
Univ.
AT
UTC+1
Eseola
Alice
Norwich
The Sainsbury Laboratory
Univ.
GB
UTC+1
Esner
Milan
Brno
Ceitec Masaryk University
Univ.
CZ
UTC+1
Fazeli
Elnaz
Helsinki
University of Turku / University of Helsinki
Univ.
FI
UTC+1
Gaudreault
Nathalie
Seattle
Allen Institute
Private lab
US
UTC-7
Gauthier
Pascal
Jonquiere
RioTinto
Private lab
CA
UTC+5
Gay
Guillaume
Marseille
France BioImaging, BioCampus, Université de Montpellier
Univ.
FR
UTC+1
Geoghegan
Niall
Coburg North
WEHI
Univ.
AU
UTC+11
Giakoumakis
Nikolaos
Barcelona
Institute for Research in Biomedicine Barcelona
Univ.
ES
UTC+1
Giang
William
Hershey
Penn State University
Univ.
US
UTC-4
Grebnev
Gleb
Heidelberg
Global BioImaging
Gov.
DE
UTC+1
Grunwald
David
Worcester
University of Massachusetts
Univ.
US
UTC-4
Guaimas
Francisco
San Martin
CONICET-UNSAM
Gov.
AR
UTC-3
Guerrero
Adan
Cuernavaca
National Autonomous University of Mexico
Univ.
MX
UTC+6
Guilbert
Thomas
Paris
RTmfm / INSERM
Univ.
FR
UTC+2
Halavatyi
Aliaksandr
Heidelberg
EMBL Heidelberg
EU-Org
DE
UTC+2
Hammer
Mathias
Worcester
University of Massachusetts Medical School
Univ.
US
UTC+5
Hartley
Matthew
Cambridge
EMBL-EBI
EU-Org
GB
UTC+1
Hatto
Mao
Prague
Nikon
Industry
CZ
UTC+2
Ho
Kenneth
London
The Francis Crick Institute
Private lab
GB
UTC+-0
Holland
Ian
Ottawa
Teledyne Lumenera
Industry
CA
UTC-8
Hu
Jianjiang
Huddinge
Karolinska Institutet
Univ.
SE
UTC+1
Huisken
Jan
Göttingen
Georg-August-Universität Göttingen
Univ.
DE
UTC+1
Ibarra
Humberto
New York
Zuckerman Institute – University of Columbia
Univ.
US
UTC-4
Kalaš
Matúš
Bergen
University of Bergen
Univ.
NO
UTC+1
Kemmer
Isabel
Heidelberg
Euro-BioImaging ERIC
EU-Org
DE
UTC+1
Kirchenbüchler
David
Chicago
Northwestern
Univ.
US
UTC-6
Kobayashi
Norio
Wako
Riken
Private lab
JP
UTC+9
Kunis
Susanne
Osnabrueck
GerBi-GMB WG 6
Univ.
DE
UTC+2
Kupcu Yoldas
Aybuke
Hinxton
EMBL-EBI
EU-Org
GB
UTC+-0
Kyoda
Koji
Kobe
RIKEN Center for Biosystems Dynamics Research
Gov.
JP
UTC+9
Lacoste
Judith
Montreal
MIA Cellavie Inc.
Industry
CA
UTC-4
Laferriere
Pascal
Nepean
Teledyne Lumenera
Industry
CA
UTC-5
Lai
Pok Yui
Oxford
University of Oxford
Univ.
GB
UTC+1
Laktiushkin
Viktor
Sochi
Sirius
Univ.
RU
UTC+3
Landua
Kalika
Houston
Nikon Instruments
Industry
US
UTC-5
Laude
Alex
Newcastle
Newcastle University
Univ.
GB
UTC+1
Le Dévédec
Sylvia
Leiden
Leiden University
Gov.
NL
UTC-2
Lee
James
Houston
Baylor College of Medicine
Univ.
US
UTC-6
Lee
Kitty
Stanford
Stanford University
Univ.
US
UTC-8
Lerksuthirat
Tassanee
Rachathewi
Mahidol Unive
Univ.
TH
UTC+7
Levitt
James
London
Nikon Imaging Centre, King’s College London, UK
Univ.
GB
UTC+-0
Li
Xiaoming
Shanghaitech
Shanghaitech University
Univ.
CN
UTC+8
Liu
Tristan
New York
Columbia University
Univ.
US
UTC-4
Lopes
Alexandre
Oeiras
IGC
Private lab
PT
UTC+-0
MA
Xiaoxiao
Singapore
ASTAR
Gov.
SG
UTC+8
Madi
Mehdi
Cachan
Abbelight
Industry
FR
UTC+1
Marcello
Marco
Liverpool
University of Liverpool
Univ.
GB
UTC+1
Mast
Fred
Seattle
Seattle Children’s Hospital
Univ.
US
UTC+8
Mateos Langerak
Julio
Montpellier
MRI
Univ.
FR
UTC+2
Mathur
Aastha
Heidelberg
Euro BioImaging
EU-Org
DE
UTC+2
Matthews
Cedric
Marseille
University of Aix-Mars.
Univ.
FR
UTC+2
McMillan
Paul
Parkville
University of Melbourne
Univ.
AU
UTC+10
Mezzano
Valeria
New York
NYU School of Medicine
Univ.
US
UTC-5
Micu
Ileana
Belfast
Queen’s University Belfast
Univ.
GB
UTC+1
Mikulski
Zbigniew
La Jolla
La Jolla Institute for Immunology
Private lab
US
UTC-8
Mohindra
Rachit
Tucson
Teledyne Photometrics
Industry
US
UTC-7
Moore
Josh
Dundee
University of Dundee
Univ.
GB
UTC+1
Nechyporuk-Zloy
Volodymyr
London
Imperial College of Science, Technology and Medicine
Univ.
GB
UTC+-0
Neumann
Sophie
Jena
FSU Jena
Univ.
DE
UTC+2
Nitschke
Roland
Freiburg
University of Freiburg, Life Imaging Center
Univ.
DE
UTC+2
Norlin
Nils
Lund
Lund University
Univ.
SE
UTC+1
ODonnell
Rob
New York
Rockefeller University Press
Univ.
US
UTC-4
Ogg
Stephen
Thuwal
King Abdullah University of Sccience & Technology
Univ.
SA
UTC+3
Onami
Shuichi
Kobe
Riken
Private lab
JP
UTC+9
Oord
Kees
Amsterdam
Nikon
Industry
NL
UTC+1
Pattison
Allister
Belfast
Andor
Industry
GB
UTC+-0
Pengo
Thomas
Minneapolis
University of Minnesota
Univ.
US
UTC-6
Pepperkok
Rainer
Heidelberg
EMBL Heidelberg
EU-Org
DE
UTC+-0
Peron-Cane
Caroline
PARIS
TELIGHT
Industry
FR
UTC+1
Piguet
Joachim
Stockholm
KTH Royal Institute of Technology
Univ.
SE
UTC+1
Pimentel
Arturo
Mexico
Biotechnology Inst.
Univ.
MX
UTC-5
Podder
Santosh
Pune
IISER Pune
Gov.
IN
UTC-8
Price
Meridith
Chapel Hill
Oxford Inst. Bitplane
Industry
US
UTC-4
Relich
Peter
Torrance
Intellisense Systems, Inc.
Univ.
US
UTC-7
Reymann
Jürgen
Mannheim
Leica
Industry
DE
UTC+2
Rhode
Sebastian
Munich
Carl Zeiss Microscopy GmbH
Industry
DE
UTC+2
Rigano
Alessandro
Worcester
UMass Chan Medical School
Univ.
US
UTC-5
Rogers
Kelly
Parkville
Walter & Eliza Hall Institute of Medical Research
Univ.
AU
UTC+10
Rosa-Molinar
Eduardo
Saint Louis
Washington University in Saint Louis School of Medicine, Washington University Center for Cellular Imaging
Univ.
US
UTC+6
Saint-Hilaire
Cadisha
Paris
Curie Institute
Univ.
FR
UTC+1
Sanders
Mark
Minneapolis
University of Minnesota
Univ.
US
UTC-5
Sanguinetti
Bruno
Zug
Dotphoton AG
Industry
CH
UTC+1
Schoonderwoert
Vincent
Hilversum
Scientific Volume Imaging BV
Industry
NL
UTC+1
Schreiner
Ryan
New York
Weill Cornell Medicine
Univ.
US
UTC-4
Schroth-Diez
Britta
Dresden
MPI-CBG
MPG
DE
UTC+2
Schuster
Aminul
London
N/A
Univ.
GB
UTC+-0
Scott
Ryan
Moffett Field
KBR/NASA Ames
Gov.
US
UTC-8
Selchow
Olaf
Gera
Microscopy & BioImaging Consulting
Industry
DE
UTC+2
Shakouri
Mahsa
Heidelberg
DKFZ
Industry
DE
UTC+12
Sherwood
Francois
Hinxton
EMBL-EBI
EU-Org
GB
UTC+-0
Shorte
Spencer
Paris
Institut Pasteur
Private lab
FR
UTC+9
Sibbons
Jane
Adelaide
University of Adelaide
Univ.
AU
UTC+9
Sisamakis
Evangelos
Berlin
PicoQuant GmbH
Industry
DE
UTC+1
Smith
Carlas
Delft
Delft University of technology
Univ.
NL
UTC+2
Srinivasan
Sathya
Beaverton
ONPRC
Univ.
US
UTC-8
Staurovsky
Susan
Farmington
UConn Health
Univ.
US
UTC-4
Strambio De Castillia
Caterina
Worcester
University of Massachusetts Medical School, Program in Molecular Medicine; Chan Zuckerberg Initiative; BINA Quality Control and Data Management Working Group
Univ.
US
UTC-4
Sudar
Damir
Oakland
Quant.Ima. Systems
Industry
US
UTC-7
Swanson
Sarah
Madison
University of Wisconsin
Univ.
US
UTC+6
Swedlow
Jason
Dundee
University ofDundee
Univ.
GB
UTC+1
Ta
Adam
Seattle
Sage Bionetworks
Private lab
US
UTC+-0
Tapia
Pablo
Bethesda
National Institutes of Health (NIH)
Gov.
US
UTC-4
Tosi
Sebastien
Copenhagen
UCPH / DBI-INFRA
Univ.
DK
UTC+1
Tourtellotte
Jocelyn
Brimfield
UMassChan
Univ.
US
UTC-4
Tsuchida
Mark
Madison
University of Wisconsin-Madison
Univ.
US
UTC-6
Tzavaras
Nikos
New York
Icahn School of Medicine at Mount Sinai
Univ.
US
UTC-5
Vasconcelos
Verónica
Coimbra
Polytechnic University of Coimbra
Univ.
PT
UTC+-0
Vierdag
Wouter-Michiel
Heidelberg
European Molecular Biology Laboratory
EU-Org
DE
UTC+2
Wagner
Darcy
Montreal
McGill University
Univ.
CA
UTC-4
Wee
Erika
Cold Spring Harbor
Cold Spring Harbor Laboratory
Univ.
US
UTC-5
Weis
Markus
Münster
Olympus Soft Imaging Solutions GmbH
Industry
DE
UTC+1
Wernet
Tobias
Freiburg
University of Freiburg, Life Imaging Center
Univ.
DE
UTC+1
West
Steven
London
Sainsbury Wellcome Centre, UCL
Univ.
GB
UTC+-0
Wiegraebe
Winfried
Seattle
Bruker
Industry
DE
UTC+8
Wilde
Geraint
Belfast
Oxford Inst. Andor
Industry
GB
UTC+1
Yunling
XU
Paris
Parcc, U970, Inserm
Univ.
FR
UTC+1
Zulueta-Coarasa
Teresa
Hinxton
EMBL-EBI
EU-Org
GB
UTC+-0
Zuschratter
Werner
Magdeburg
Leibniz-Institut für Neurobiologie – LIN
Leibniz
DE
UTC+2