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, 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 currently active focussed subgroups are:
- Subgroup 1: 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 Nietschke
- Contact information: caterina.strambio@umassmed.edu
- Cloud storage location (can be accessed as a member) → here
- Subgroup 2: 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 3: 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.com and kenneth.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 4: 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
- Cloud storage location (can be accessed as a member) → here
To join one or more of the groups you need to first become a member of QUAREP-LiMi here, where you can select WG7 as one of the Work Groups you want to participate in. Once you have access to the cloud server, you can enter your name in this spreadsheet to join the respective subgroups.
WG 7 - Co-Chairs
WG 7 - Latest News
Last meeting: 20th June 2022, 5:00 pm
To gain access to the full meeting minutes, you have to be a registered member of QUAREP-LiMi. Use the “Become a Member” form or write an e-mail to the WG chair.
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
Memberlist WG 7
Last name First Name Town Organisation Affiliation Lab Affiliation Country Mail address Time Zone
Acton
Sydney
Mobile
University of South Alabama
Univ.
US
sydneyacton@southalabama.edu
UTC-6
Alexopoulos
Ioannis
Giessen
CIGL Imaging Unit
Univ.
DE
Ioannis.Alexopoulos@innere.med.uni-giessen.de
UTC+2
Bagley
Steve
Manchester
Univ. Manch.
Univ.
GB
steven.bagley-2@manchester.ac.uk
UTC+1
Bain
Virginia
Danvers
Cell Signaling Technology
Industry
US
virginia.bain@cellsignal.com
UTC-5
Bassi
Andrea
Milano
Politecnico di Milano
Univ.
IT
andrea1.bassi@polimi.it
UTC+2
Beckert
Hannes
Bonn
GerBi-GMB WG 1
Univ.
DE
hannes.beckert@ukbonn.de
UTC+2
Biehlmaier
Oliver
Basel
Imaging Core Facility, Biozentrum, Basel
Univ.
CH
oliver.biehlmaier@unibas.ch
UTC+1
Boehm
Ulrike
Oberkochen
Zeiss
Industry
DE
ulrike.boehm@zeiss.com
UTC-4
Bourg
Nicolas
Cachan
Abbelight
Industry
FR
nbourg@abbelight.com
UTC+1
Breitlow
Juergen
Berlin
PicoQuant GmbH
Industry
DE
breitlow@picoquant.com
UTC+1
Carvalho
Mariana
Braga
INL – International Iberian Nanotechnology Laboratory
EU-Org
PT
mariana.carvalho@inl.int
UTC+-0
Casas-Moreno
Xavier
Solna
KTH Royal Institute of Technology
Univ.
SE
xaviercm@kth.se
UTC+1
Cebecauer
Marek
J. Heyrovsky Institute of Physical Chemistry
Gov.
CZ
marek.cebecauer@jh-inst.cas.cz
UTC+1
Chacko
Jenu
Madison
University of Wisconsin Madison
Univ.
US
jenu.chacko@wisc.edu
UTC-6
Chambers
James
Boston
BINA
Univ.
US
jjchambe@umass.edu
UTC-4
Cole
Louise
Sydney
Univ. Technology
Univ.
AU
Louise.Cole@uts.edu.au
UTC+11
Conde-Sousa
Eduardo
Porto
INEB/i3S
Univ.
PT
econdesousa@gmail.com
UTC+0
Condon
Nicholas
Brisbane
The University of Queensland
Univ.
AU
n.condon@uq.edu.au
UTC+10
Dobbie
Ian
Boston
Johns Hopkins Unibversity
Univ.
US
ian.dobbie@jhu.edu
UTC+5
Ebeling
Carl
Salt Lake City
Recursion Pharma
Industry
US
carl.ebeling@recursionpharma.com
UTC-6
Ecker
Rupert
Vienna
TissueGnostics GmbH
Univ.
AT
rupert.ecker@tissuegnostics.com
UTC+1
Esner
Milan
Brno
Ceitec Masaryk University
Univ.
CZ
milan.esner@ceitec.muni.cz
UTC+1
Fazeli
Elnaz
Helsinki
University of Turku/ University of Helsinki
Univ.
FI
elnaz.fazeli@helsinki.fi
UTC+1
Gaudreault
Nathalie
Seattle
BINA
Private lab
US
nathalieg@alleninstitute.org
UTC-7
Gauthier
Pascal
Jonquiere
RioTinto
Private lab
CA
pascal.gauthier4@riotinto.com
UTC+5
Gay
Guillaume
Marseille
France BioImaging, BioCampus, Université de Montpellier
Univ.
FR
guillaume.gay@lirmm.fr
UTC+1
Giang
William
Atlanta
Penn State University
Univ.
US
wgiang@pennstatehealth.psu.edu
UTC-4
Grebnev
Gleb
Heidelberg
Global BioImaging
Gov.
DE
gleb.grebnev@embl.de
UTC+1
Grunwald
David
Worcester
Univ. of Massachusetts
Univ.
US
david.grunwald@umassmed.edu
UTC-4
Guilbert
Thomas
Paris
RTmfm / INSERM
Univ.
FR
thomas.guilbert@inserm.fr
UTC+2
Halavatyi
Aliaksandr
Heidelberg
EMBL Heidelberg
EU-Org
DE
aliaksandr.halavatyi@embl.de
UTC+2
Hammer
Mathias
Worcester
University of Massachusetts Medical School
Univ.
US
mathias.hammer@umassmed.edu
UTC+5
Hartley
Matthew
Cambridge
EMBL-EBI
EU-Org
GB
matthewh@ebi.ac.uk
UTC+1
Hatto
Mao
Praha 5
Nikon
Industry
CZ
mao.hatto@nikon.com
UTC+2
Ho
Kenneth
London
The Francis Crick Institute
Private lab
GB
kenneth.ho@crick.ac.uk
UTC+-0
Holland
Ian
Ottawa
Teledyne Lumenera
Industry
CA
ian.holland@teledyne.com
UTC-8
Huisken
Jan
Göttingen
Georg-August-Universität Göttingen
Univ.
DE
jan.huisken@uni-goettingen.de
UTC+1
Kirchenbüchler
David
Chicago
Northwestern
Univ.
US
david.kirchenbuchler@northwestern.edu
UTC-6
Kobayashi
Norio
Wako
Riken
Private lab
JP
norio.kobayashi@riken.jp
UTC+9
Kunis
Susanne
Osnabrueck
GerBi-GMB WG 6
Univ.
DE
sukunis@uos.de
UTC+2
Kyoda
Koji
Kobe
RIKEN Center for Biosystems Dynamics Research
Gov.
JP
kkyoda@riken.jp
UTC+9
Laferriere
Pascal
Nepean
Teledyne Lumenera
Industry
CA
pascal.laferriere@teledyne.com
UTC-5
Laktiushkin
Viktor
Sochi
Sirius
Univ.
RU
victoriousf@gmail.com
UTC+3
Laude
Alex
Newcastle
Newcastle University
Univ.
GB
alex.laude@ncl.ac.uk
UTC+1
Le Dévédec
Sylvia
Leiden
Leiden University
Gov.
NL
s.e.ledevedec@lacdr.leidenuniv.nl
UTC-2
Lee
Kitty
Stanford
Stanford University
Univ.
US
kamanl@stanford.edu
UTC-8
Levitt
James
London
Nikon Imaging Centre, King’s College London, UK
Univ.
GB
james.levitt@kcl.ac.uk
UTC+-0
Li
Xiaoming
Shanghaitech
Shanghaitech University
Univ.
CN
Lixm@shanghaitech.edu.cn
UTC+8
Lopes
Alexandre
Oeiras
IGC
Private lab
PT
alopes@igc.gulbenkian.pt
UTC+-0
Marcello
Marco
Liverpool
Univ. Liverpool
Univ.
GB
m.marcello@liv.ac.uk
UTC+1
Mast
Fred
Seattle
Seattle Children’s Hospital
Univ.
US
Fred.Mast@seattlechildrens.org
UTC+8
Mateos-Langerak
Julio
Montpellier
MRI
Univ.
FR
julio.mateos-langerak@igh.cnrs.fr
UTC+2
Mathur
Aastha
Heidelberg
Euro BioImaging
EU-Org
DE
aastha.mathur@embl.de
UTC+2
Matthews
Cedric
Marseille
Univ. Aix-Mars.
Univ.
FR
cedric.matthews@univ-amu.fr
UTC+2
Micu
Ileana
Belfast
Queen’s University Belfast
Univ.
GB
i.micu@qub.ac.uk
UTC+1
Mikulski
Zbigniew
La Jolla
La Jolla Institute for Immunology
Private lab
US
zmikulski@lji.org
UTC-8
Mohindra
Rachit
Tucson
Teledyne Photometrics
Industry
US
rachit.mohindra@teledyne.com
UTC-7
Moore
Joshua
Dundee
Univ. of Dundee
Univ.
GB
j.a.moore@dundee.ac.uk
UTC+1
Nitschke
Roland
Freiburg
GerBi-GMB WG 1
Univ.
DE
Roland.Nitschke@uni-freiburg.de
UTC+2
Norlin
Nils
Lund
Lund University
Univ.
SE
nils.norlin@gmail.com
UTC+1
ODonnell
Rob
New York
Rockefeller University Press
Univ.
US
odonner@rockefeller.edu
UTC-4
Ogg
Steve
Thuwal
KAUST
Univ.
SA
stephen.ogg@kaust.edu.sa
UTC+3
Onami
Shuichi
Kobe
Riken
Private lab
JP
sonami@riken.jp
UTC+9
Pengo
Thomas
Minneapolis
University of Minnesota
Univ.
US
tpengo@umn.edu
UTC-6
Pepperkok
Rainer
Heidelberg
EMBL Heidelberg
EU-Org
DE
pepperko@embl.de
UTC+-0
Pimentel
Arturo
Mexico
Biotechnology Inst.
Univ.
MX
arturo.pimentel@mail.ibt.unam.mx
UTC-5
Podder
Santosh
Pune
IISER Pune
Gov.
IN
santosh.p@iiserpune.ac.in
UTC-8
Powers
Ann
Worcester
UMass Chan Medical School
Univ.
US
ann.powers@umassmed.edu
UTC+4
Price
Meridith
Chapel Hill
Oxford Inst. Bitplane
Industry
US
meredith.price@bitplane.com
UTC-4
Relich
Peter
Torrance
Intellisense Systems, Inc.
Univ.
US
prelich@intellisenseinc.com
UTC-7
Reymann
Jürgen
Mannheim
Leica
Industry
DE
Juergen.Reymann@leica-microsystems.com
UTC+2
Rezgui
Rachid
Abu Dhabi
NYU Abu Dhabi
Univ.
AE
rachid.rezgui@nyu.edu
UTC+4
Rhode
Sebastian
Munich
Carl Zeiss Microscopy GmbH
Industry
DE
sebastian.rhode@zeiss.com
UTC+2
Rigano
Alessandro
Worcester
UMass Chan Medical School
Univ.
US
alex.rigano@umassmed.edu
UTC-5
Rogers
Kelly
Parkville
Walter & Eliza Hall Institute of Medical Research
Univ.
AU
rogers@wehi.edu.au
UTC+10
Saint-Hilaire
Cadisha
Paris
Curie Institute
Univ.
FR
sainthilaire.cadisha@gmail.com
UTC+1
Sanders
Mark
Minneapolis
University of Minnesota
Univ.
US
msanders@umn.edu
UTC-5
Sanguinetti
Bruno
Zug
Dotphoton AG
Industry
CH
bruno.sanguinetti@dotphoton.com
UTC+1
Schoonderwoert
Vincent
Hilversum
Scientific Volume Imaging
Industry
NL
vincent@svi.nl
UTC+1
Schreiner
Ryan
New York
Weill Cornell Medicine
Univ.
US
ryanschreiner@gmail.com
UTC-4
Scott
Ryan
Moffett Field
Ames Life Sciences Data Archive/KBR/NASA Ames
Gov.
US
ryan.t.scott@nasa.gov
UTC-8
Selchow
Olaf
Gera
Microscopy & BioImaging Consulting
Industry
DE
oselchow@gmail.com
UTC+2
Shorte
Spencer
Paris
Institut Pasteur
Private lab
FR
spencer.shorte@pasteur.fr
UTC+9
Sisamakis
Evangelos
Berlin
PicoQuant GmbH
Industry
DE
sisamakis@picoquant.com
UTC+1
Smadja
Michel
Asnières
Sis’nCom
Industry
FR
michel.smadja@gmail.com
UTC+2
Smith
Carlas
Delft
Delft University of technology
Univ.
NL
c.s.smith@tudelft.nl
UTC+2
Sousa
Mafalda
Porto
I3S ALM
Private lab
PT
mafsousa@ibmc.up.pt
UTC+-0
Srinivasan
Sathya
Beaverton
ONPRC
Univ.
US
scitecheditor@gmail.com
UTC-8
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
caterina.strambio@umassmed.edu
UTC-4
Sudar
Damir
Oakland
Quant.Ima. Systems
Industry
US
dsudar@qitissue.com
UTC-7
Swedlow
Jason
Dundee
Univ. of Dundee
Univ.
GB
j.r.swedlow@dundee.ac.uk
UTC+1
Tsuchida
Mark
Madison
University of Wisconsin–Madison
Univ.
US
matsuchida@wisc.edu
UTC-6
van der Oord
Kees
Amsterdam
Nikon
Industry
NL
Kees.van.der.Oord@nikon.com
UTC+1
Wee
Erika
Cold Spring Harbor
Cold Spring Harbor Laboratory
Univ.
US
wee@cshl.edu
UTC-5
Weis
Markus
Münster
Olympus Soft Imaging Solutions GmbH
Industry
DE
Markus.Weis@olympus.com
UTC+1
Wernet
Tobias
Freiburg
Albert Ludwigs University Freiburg
Univ.
DE
tobias.wernet@biologie.uni-freiburg.de
UTC+1
Wiegraebe
Winfried
Seattle
Bruker
Industry
DE
winfried.wiegraebe@bruker.com
UTC+8
Wilde
Geraint
Belfast
Oxford Inst. Andor
Industry
GB
g.wilde@andor.com
UTC+1
Zuschratter
Werner
Magdeburg
GerBi-GMB WG 1
Leibniz
DE
Werner.Zuschratter@lin-magdeburg.de
UTC+2

12th meeting, 21st of February 2022
Meeting date
Meeting summary
- Revision of the WG7 main webpage on QUAREP.org
- Review progress done with WG2 to revise the Camera section of 4DN-BINA-OME-(QUAREP) Microscopy Metadata model in collaboration with Camera manufacturers and members of the Camera community.
- Review progress of SubGroup 2 (Metadata Education) and SubGroup 3 (Metadata Storage Specifications).
- Reminder: the novel SubGroup 4 (Model Revision) was formed but it did not convene yet because they are waiting for the end of the first phase of Camera community conversations. Please join us in this important work.