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CITATION.cff
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cff-version: 1.2.0
message: "If you use content of this repository, please cite it using these metadata. Authors are in alphabetical order!"
repository: "https://github.com/NFDI4BIOIMAGE/Cologne-Hackathon-2023"
authors:
- affiliation: Department of Biology/Chemistry and Center for Cellular Nanoanalytics, University Osnabrück, Germany
alias: MM-abdrabbou
city: Osnabrück
country: DE
family-names: Abdrabbou
given-names: Mohamed M.
orcid: "https://orcid.org/0000-0003-2778-7483"
- affiliation: Center for Molecular Medicine Cologne and CECAD Research Center, University of Cologne, Cologne, Germany
alias: mmb24
city: Cologne
country: DE
family-names: Babaki
given-names: Mehrnaz
orcid: "https://orcid.org/0000-0003-3099-618X"
- affiliation: Center for Advanced Imaging, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
alias: Tom-TBT
city: Düsseldorf
country: DE
family-names: Boissonnet
given-names: Tom
orcid: "https://orcid.org/0000-0002-3328-9467"
- affiliation: Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
alias: MicheleBortol
city: Heidelberg
country: DE
family-names: Bortolomeazzi
given-names: Michele
orcid: "https://orcid.org/0000-0001-5805-5774"
- affiliation: Regional Computer Center (RRZK), University of Cologne, Cologne, Germany
alias: eik-dahms
city: Cologne
country: DE
family-names: Dahms
given-names: Eik
orcid: "https://orcid.org/0000-0002-7452-1146"
- affiliation: Center for Advanced Imaging, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
alias: VAFuchs
city: Düsseldorf
country: DE
family-names: Fuchs
given-names: Vanessa A. F.
orcid: "https://orcid.org/0000-0002-4101-6987"
- affiliation: Regional Computing Centre (RRZK/ITCC), University of Cologne, Cologne, Germany
city: Cologne
country: DE
email: [email protected]
family-names: Hoevels
given-names: Moritz
- affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
alias: Nirkan
city: Cologne
country: DE
family-names: Kandpal
given-names: Niraj
orcid: "https://orcid.org/0009-0007-5101-4786"
- affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
alias: cmohl2013
city: Bonn
country: DE
family-names: Möhl
given-names: Christoph
orcid: "https://orcid.org/0000-0002-0829-5101"
- affiliation: German BioImaging—Society for Microscopy and Image Analysis e.V., Constance, Germany
alias: joshmoore
city: Constance
country: DE
family-names: Moore
given-names: Joshua A.
orcid: "https://orcid.org/0000-0003-4028-811X"
- affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
alias: AstridSchauss
city: Cologne
country: DE
family-names: Schauss
given-names: Astrid
orcid: "https://orcid.org/0000-0002-6658-2192"
- affiliation: Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
alias: andreaschrader
city: Cologne
country: DE
family-names: Schrader
given-names: Andrea
orcid: "https://orcid.org/0000-0002-3879-7057"
- affiliation: Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
alias: tstoeter
city: Magdeburg
country: DE
family-names: Stöter
given-names: Torsten
- affiliation: Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany
alias: JThoennissen
city: Jülich
country: DE
family-names: Thönnißen
given-names: Julia
orcid: "https://orcid.org/0000-0002-5467-871X"
- affiliation: Regional Computer Center (RRZK), University of Cologne, Cologne, Germany
alias: mvals
city: Cologne
country: DE
family-names: Valencia-S.
given-names: Monica
orcid: "https://orcid.org/0000-0003-3430-2683"
- affiliation: Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
alias: HLWeil
city: Kaiserslautern
country: DE
family-names: Weil
given-names: H. Lukas
orcid: "https://orcid.org/0000-0003-1945-6342"
- affiliation: Muenster Imaging Network, University of Muenster, Muenster, Germany
alias: JensWendt
city: Muenster
country: DE
family-names: Wendt
given-names: Jens
orcid: "https://orcid.org/0009-0002-1826-7099"
- affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
alias: pzentis
city: Cologne
country: DE
family-names: Zentis
given-names: Peter
orcid: "https://orcid.org/0000-0002-6999-132X"
date-released: "2023-12-07"
keywords:
- OMERO
- ARC
- Neuroglancer
- zarr
- REMBI
- metadata
- use cases
- multimodal data
- hackathon
- NFDI4Bioimage
- DataPLANT
- CECAD
- CEPLAS
- CRC-TRR341
license: CC-BY-4.0
title: NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne-Hackathon-2023, repository)
version: 1.0.1
references:
- authors:
- family-names: Allen
given-names: Chris
- family-names: Burel
given-names: Jean-Marie
- family-names: Moore
given-names: Joshua A.
- family-names: Blackburn
given-names: Colin
- family-names: Linkert
given-names: Melissa
- family-names: Loynton
given-names: Scott
- family-names: MacDonald
given-names: Donald
- family-names: Moore
given-names: William J.
- family-names: Neves
given-names: Carlos
- family-names: Patterson
given-names: Andrew
- family-names: Porter
given-names: Michael
- family-names: Tarkowska
given-names: Aleksandra
- family-names: Loranger
given-names: Brian
- family-names: Avondo
given-names: Jerome
- family-names: Lagerstedt
given-names: Ingvar
- family-names: Lianas
given-names: Luca
- family-names: Leo
given-names: Simone
- family-names: Hands
given-names: Katherine
- family-names: Hay
given-names: Ron T.
- family-names: Patwardhan
given-names: Ardan
- family-names: Best
given-names: Christoph
- family-names: Kleywegt
given-names: Gerard J.
- family-names: Zanetti
given-names: Gianluigi
- family-names: Swedlow
given-names: Jason R.
date-published: "2012-02-28"
doi: 10.1038/nmeth.1896
end: 253
issue: 3
journal: Nature Methods
scope: "A reference for OMERO - model-driven data management for experimental biology."
start: 245
title: "OMERO: flexible, model-driven data management for experimental biology"
type: article
url: "https://doi.org/10.1038/nmeth.1896"
volume: 9
- authors:
- family-names: Anders
given-names: Ivonne
- family-names: Bianchi
given-names: Christophe
- family-names: Broder
given-names: Daan
- family-names: Hellström
given-names: Maggie
- family-names: Islam
given-names: Sharif
- family-names: Jejkal
given-names: Thomas
- family-names: Lannom
given-names: Larry
- family-names: Peters-von Gehlen
given-names: Karsten
- family-names: Quick
given-names: Robert
- family-names: Schlemmer
given-names: Alexander
- family-names: Schwardmann
given-names: Ulrich
- family-names: Soiland-Reyes
given-names: Stian
- family-names: Strawn
given-names: George
- family-names: van Uytvanck
given-names: Dieter
- family-names: Weiland
given-names: Claus
- family-names: Wittenburg
given-names: Peter
- family-names: Zwölf
given-names: Carlo
date-released: "2023-01-12"
doi: 10.5281/zenodo.7782262
license: CC-BY-4.0
publisher: Zenodo
scope: "Reference for FAIR digital objects as mentioned in the introduction when giving the context for this hackathon with respect to ARCs."
title: "FDO Forum FDO Requirement Specifications"
type: article
url: "https://doi.org/10.5281/zenodo.7782262"
version: "3.0"
year: 2023
- authors:
- family-names: Baker
given-names: Steve
- name: "tree contributors"
date-accessed: "2023-12-07"
license: GPL-2.0
repository: "https://github.com/Old-Man-Programmer/tree"
scope: "Used to create the file tree in the README provided as an overview of the repository."
title: tree
type: software
url: "https://oldmanprogrammer.net/source.php?dir=projects/tree"
version: v2.1.1
year: 2023
- authors:
- family-names: Burel
given-names: Jean-Marie
- family-names: Moore
given-names: Joshua A.
- family-names: Moore
given-names: William J.
copyright: "(C) 2022-2023, The Open Microscopy Environment"
license: AGPL-3.0
repository: "https://github.com/ome/omero-web-zarr"
scope: "omero-web-zarr v0.1.1 was used in the Neuroglancer topic including OMERO / zarr."
title: ome/omero-web-zarr 0.1.1 (GitHub repository)
type: software
version: v0.1.1
year: 2023
- authors:
- name: "Coderefinery contributors"
date-accessed: "2024-01-03"
license: CC-BY-4.0
repository: "https://github.com/coderefinery/github-without-command-line"
scope: "The repository is submitted to Zenodo as described in these instructions."
title: github-without-command-line/doi
type: website
url: "https://coderefinery.github.io/github-without-command-line/doi/"
year: 2020
- authors:
- family-names: Crusoe
given-names: Michael R
- family-names: Abeln
given-names: Sanne
- family-names: Iosup
given-names: Alexandru
- family-names: Amstutz
given-names: Peter
- family-names: Chilton
given-names: John
- family-names: Tijanić
given-names: Nebojša
- family-names: Ménager
given-names: Hervé
- family-names: Soiland-Reyes
given-names: Stian
- family-names: Gavrilović
given-names: Bogdan
- family-names: Goble
given-names: Carole
- name: The CWL Community
doi: 10.1145/3486897
end: 63
issn: "1557-7317"
journal: Communications of the ACM
license: CC-BY-4.0
number: 6
publisher: Association for Computing Machinery (ACM)
scope: "Reference for Common Workflow Language as mentioned in the introduction when giving the context for this hackathon with respect to ARCs."
start: 54
title: "Methods included: standardizing computational reuse and portability with the Common Workflow Language"
type: article
url: "http://dx.doi.org/10.1145/3486897"
volume: 65
year: 2022
- authors:
- name: "DataPLANT community"
date-accessed: "2023-11-38"
license: CC-BY-4.0
repository: "https://github.com/nfdi4plants/ARC-specification"
scope: "The ARC specification underlying the conceptual discussions and setup towards OMERO-ARC interoperability."
title: "nfdi4plants/ARC-specification: 1.2"
type: software
url: "https://doi.org/10.5281/zenodo.10091038"
version: v1.2
year: 2023
- authors:
- family-names: Dumschott
given-names: Kathryn
- family-names: Dörpholz
given-names: Hannah
- family-names: Laporte
given-names: Marie-Angélique
- family-names: Brilhaus
given-names: Dominik
- family-names: Schrader
given-names: Andrea
- family-names: Usadel
given-names: Björn
- family-names: Neumann
given-names: Steffen
- family-names: Arnaud
given-names: Elizabeth
- family-names: Kranz
given-names: Angela
date-published: "2023-11-30"
doi: 10.3389/fpls.2023.1279694
issn: "1664-462X"
journal: Frontiers in Plant Science
scope: "Ontologies suited for plant research data annotation as prepared in the used imaging ARC in the REMBI - Mapping topic."
title: "Ontologies for increasing the FAIRness of plant research data"
type: article
url: "https://www.frontiersin.org/articles/10.3389/fpls.2023.1279694"
volume: 14
year: 2023
- authors:
- family-names: Fedorov
given-names: Andriy
- family-names: Beichel
given-names: Reinhard
- family-names: Kalpathy-Cramer,
given-names: Jayashree
- family-names: Finet
given-names: Julien
- family-names: Fillion-Robin
given-names: Jean-Christophe
- family-names: Pujol
given-names: Sonia
- family-names: Bauer
given-names: Christian
- family-names: Jennings
given-names: Dominiqu
- family-names: Fennessy
given-names: Fiona
- family-names: Sonka
given-names: Milan
- family-names: Buatti
given-names: John
- family-names: Aylward
given-names: Stephen
- family-names: Miller
given-names: James V.
- family-names: Pieper
given-names: Steve
- family-names: Kikinis
given-names: Ron
doi: 10.1016/j.mri.2012.05.001
end: 1341
issue: 9
journal: Magnetic Resonance Imaging
scope: "3D Slicer was mentioned in the introduction when giving context for this hackathon although it was not worked on in the finally chosen topics."
start: 1323
title: "3D Slicer as an Image Computing Platform for the Quantitative Imaging Network"
type: article
url: "https://www.slicer.org/"
volume: 30
year: 2012
- authors:
- family-names: Frey
given-names: Kevin
- name: "Swate contributors"
license: MIT
repository: "https://github.com/nfdi4plants/Swate"
scope: "Used for annotating an imaging experiment with respective ontologies."
title: "Swate v0.6.2 (GitHub repository)"
type: software
version: v0.6.2
year: 2022
- authors:
- name: "Google Connectomics Team"
license: Apache-2.0
repository: "https://github.com/google/neuroglancer/"
scope: "Used in the neuroglancer topic."
title: "Neuroglancer v2.37 (GitHub repository))"
type: software
version: v2.37
year: 2023
- authors:
- family-names: Gorgolewski
given-names: Krzysztof J.
- family-names: Auer
given-names: Tibor
- family-names: Calhoun
given-names: Vince D.
- family-names: Craddock
given-names: R. Cameron
- family-names: Das
given-names: Samir
- family-names: Duff
given-names: Eugene P.
- family-names: Flandin
given-names: Guillaume
- family-names: Ghosh
given-names: Satrajit S.
- family-names: Glatard
given-names: Tristan
- family-names: Halchenko
given-names: Yaroslav O.
- family-names: Handwerker
given-names: Daniel A.
- family-names: Hanke
given-names: Michael
- family-names: Keator
given-names: David
- family-names: Li
given-names: Xiangrui
- family-names: Michael
given-names: Zachary
- family-names: Maumet
given-names: Camille
- family-names: Nichols
given-names: B. Nolan
- family-names: Nichols
given-names: Thomas E.
- family-names: Pellman
given-names: John
- family-names: Poline
given-names: Jean-Baptiste
- family-names: Rokem
given-names: Ariel
- family-names: Schaefer
given-names: Gunnar
- family-names: Sochat
given-names: Vanessa
- family-names: Triplett
given-names: William
- family-names: Turner
given-names: Jessica A.
- family-names: Varoquaux
given-names: Gaël
- family-names: Poldrack
given-names: Russell A.
date-published: "2016-06-21"
doi: 10.1038/sdata.2016.44
end: 4463
journal: Scientific Data
issue: 1
scope: "BIDS was covered in the introduction when giving context to this hackathon and by an introductory talk. ARC-BIDS interoperability has been considered before for work at the CoRDI2023 by NFDI4Bioimage TA3 members."
start: 2052
title: "The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments"
type: article
url: "https://doi.org/10.1038/sdata.2016.44"
volume: 3
year: 2016
- authors:
- family-names: Linkert
given-names: Melissa
- family-names: Rueden
given-names: Curtis T.
- family-names: Allen
given-names: Chris
- family-names: Burel
given-names: Jean-Marie
- family-names: Moore
given-names: William J.
- family-names: Patterson
given-names: Andrew
- family-names: Loranger
given-names: Brian
- family-names: Moore
given-names: Joshua A.
- family-names: Neves
given-names: Carlos
- family-names: MacDonald
given-names: Donald
- family-names: Tarkowska
given-names: Aleksandra
- family-names: Sticco
given-names: Caitlin
- family-names: Hill
given-names: Emma
- family-names: Rossner
given-names: Mike
- family-names: Eliceiri
given-names: Kevin W.
- family-names: Swedlow
given-names: Jason R.
doi: 10.1083/jcb.201004104
end: 782
journal: The Journal of Cell Biology
number: 5
scope: "Bio Formats citation. Enables OMERO and other applications to read from and write to various file formats."
start: 777
title: "Metadata matters: access to image data in the real world"
type: article
url: "https://doi.org/10.1083/jcb.201004104"
volume: 189
year: 2010
- authors:
- family-names: Maitin-Shepard
given-names: Jeremy
- family-names: Baden
given-names: Alex
- family-names: Silversmith
given-names: William
- family-names: Perlman
given-names: Eric
- family-names: Collman
given-names: Forrest
- family-names: Blakely
given-names: Tim
- family-names: Funke
given-names: Jan
- family-names: Jordan
given-names: Chris
- family-names: Falk
given-names: Ben
- family-names: Kemnitz
given-names: Nico
- family-names: tingzhao
alias: tingzhao
- family-names: Roat
given-names: Chris
- family-names: Castro
given-names: Manuel
- family-names: Jagannathan
given-names: Sridhar
- family-names: moenigin
- alias: moenigin
- family-names: Clements
given-names: Jody
- family-names: Hoag
given-names: Austin
- family-names: Katz
given-names: Bill
- family-names: Parsons
given-names: Dave
- family-names: Wu
given-names: Jingpeng
- family-names: Kamentsky
given-names: Lee
- family-names: Chervakov
given-names: Pavel
- family-names: Hubbard
given-names: Philip
- family-names: Berg
given-names: Stuart
- family-names: Hoffer
given-names: John
- family-names: Halageri
given-names: Akhilesh
- family-names: Machacek
given-names: Christian
- family-names: Mader
given-names: Kevin
- family-names: Roeder
given-names: Lutz
- family-names: Li
given-names: Peter H.
date-released: "2021-10-16"
doi: 10.5281/zenodo.5573294
license: Apache-2.0
publisher: Zenodo
repository: "https://github.com/google/neuroglancer/"
scope: "Zenodo publication of an earlier version of the neuroglancer as the one used in the neuroglancer topic."
title: "google/neuroglancer: (v2.23)"
type: software
url: https://doi.org/10.5281/zenodo.5573294
version: v2.23
year: 2021
- authors:
- family-names: Martins Ratamero
given-names: Erick
- family-names: Burel
given-names: Jean-Marie
- family-names: Sobolewski
given-names: Peter
- family-names: Moore
given-names: William J.
doi: 10.5281/zenodo.8383499
license: GPL-2.0
repository: "https://github.com/ome/omero-cli-transfer"
scope: "omero-cli-transfer is used in OMERO_ARC interoperability which was mainly covered here in a conceptual way in the interoperability topic and also by the OMERO-ARC plugin of C. Möhl for the omero-cli-transfer."
title: "ome/omero-cli-transfer: 0.8.0 - new `--simple` option in `pack` (0.8.0)"
type: software
url: https://doi.org/10.5281/zenodo.8383499
version: v0.8.0
year: 2023
- authors:
- family-names: Möhl
given-names: Christoph
license: GPL-3.0
repository: "https://github.com/cmohl2013/omero-arc"
scope: "Plugin for omero-cli-transfer for OMERO-ARC export."
title: "OMERO-ARC Plugin (GitHub repository)"
type: software
version: v0.0.1
year: 2023
- authors:
- family-names: Moore
given-names: Joshua A.
- family-names: Basurto-Lozada
given-names: Daniela
- family-names: Besson
given-names: Sébastien
- family-names: Bogovic
given-names: John
- family-names: Bragantini
given-names: Jordão
- family-names: Brown
given-names: Eva M.
- family-names: Burel
given-names: Jean-Marie
- family-names: Casas Moreno
given-names: Xavier
- family-names: de Medeiros
given-names: Gustavo
- family-names: Diel
given-names: Erin E.
- family-names: Gault
given-names: David
- family-names: Ghosh
given-names: Satrajit S.
- family-names: Gold
given-names: Ilan
- family-names: Halchenko
given-names: Yaroslav O.
- family-names: Hartley
given-names: Matthew
- family-names: Horsfall
given-names: Dave
- family-names: Keller
given-names: Mark S.
- family-names: Kittisopikul
given-names: Mark
- family-names: Kovacs
given-names: Gabor
- family-names: Küpcü Yoldaş
given-names: Aybüke
- family-names: Kyoda
given-names: Koji
- family-names: le Tournoulx de la Villegeorges
given-names: Albane
- family-names: Li
given-names: Tong
- family-names: Liberali
given-names: Prisca
- family-names: Lindner
given-names: Dominik
- family-names: Linkert
given-names: Melissa
- family-names: Lüthi
given-names: Joel
- family-names: Maitin-Shepard
given-names: Jeremy
- family-names: Manz
given-names: Trevor
- family-names: Marconato
given-names: Luca
- family-names: McCormick
given-names: Matthew
- family-names: Lange
given-names: Merlin
- family-names: Mohamed
given-names: Khaled
- family-names: Moore
given-names: William
- family-names: Norlin
given-names: Nils
- family-names: Ouyang
given-names: Wei
- family-names: Özdemir
given-names: Bugra
- family-names: Palla
given-names: Giovanni
- family-names: Pape
given-names: Constantin
- family-names: Pelkmans
given-names: Lucas
- family-names: Pietzsch
given-names: Tobias
- family-names: Preibisch
given-names: Stephan
- family-names: Prete
given-names: Martin
- family-names: Rzepka
given-names: Norman
- family-names: Samee
given-names: Sameeul
- family-names: Schaub
given-names: Nicholas
- family-names: Sidky
given-names: Hythem
- family-names: Solak
given-names: Ahmet Can
- family-names: Stirling
given-names: David R.
- family-names: Striebel
given-names: Jonathan
- family-names: Tischer
given-names: Christian
- family-names: Toloudis
given-names: Daniel
- family-names: Virshup
given-names: Isaac
- family-names: Walczysko
given-names: Petr
- family-names: Watson
given-names: Alan M.
- family-names: Weisbart
given-names: Erin
- family-names: Wong
given-names: Frances
- family-names: Yamauchi
given-names: Kevin A.
- family-names: Bayraktar
given-names: Omer
- family-names: Cimini
given-names: Beth A.
- family-names: Gehlenborg
given-names: Nils
- family-names: Haniffa
given-names: Muzlifah
- family-names: Hotaling
given-names: Nathan
- family-names: Onami
given-names: Shuichi
- family-names: Royer
given-names: Loic A.
- family-names: Saalfeld
given-names: Stephan
- family-names: Stegle
given-names: Oliver
- family-names: Theis
given-names: Fabian J.
- family-names: Swedlow
given-names: Jason R.
date-released: "2023-09-01"
doi: 10.1007/s00418-023-02209-1
end: 251
issue: 3
journal: Histochemistry and Cell Biology
scope: "OME-Zarr reference, a fle format intending to solve image specific file format problems and used in the neuroglancer part of this hackathon."
start: 223
title: "OME-Zarr: a cloud-optimized bioimaging file format with international community support"
type: article
url: "https://doi.org/10.1007/s00418-023-02209-1"
volume: 160
year: 2023
- authors:
- name: RDM4mic
license: CC-BY-4.0
scope: "Videos suggested as an introduction along the installation to quickly capture the ideas and procedures of OMERO from the ARC contributor's perspective."
title: "I3D:bio's OMERO Training Videos 2023"
type: video
url: "https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU"
year: 2023
- authors:
- affiliation: Oxford e-Research Centre, University of Oxford, UK
family-names: Sansone
given-names: Susanna-Assunta
- affiliation: Oxford e-Research Centre, University of Oxford, UK
family-names: Rocca-Serra
given-names: Philippe
- affiliation: Oxford e-Research Centre, University of Oxford, UK
family-names: Gonzalez-Beltran
given-names: Alejandra
- affiliation: Oxford e-Research Centre, University of Oxford, UK
family-names: Johnson
given-names: David
- name: ISA Community
date-released: "2016-10-28"
doi: 10.5281/zenodo.163640
license: CC-BY-4.0
publisher: Zenodo
repository: "https://github.com/ISA-tools/isa-specs"
scope: "ARC metadata is based on the isa model which also needs to be considered in OMERO-ARC interoperability."
title: ISA Model and Serialization Specifications 1.0
type: technical note
version: 1.0
year: 2016
- authors:
- family-names: Sarkans
given-names: Ugis
- family-names: Chiu
given-names: Wah
- family-names: Collinson
given-names: Lucy
- family-names: Darrow
given-names: Michele C.
- family-names: Ellenberg
given-names: Jan
- family-names: Grunwald
given-names: David
- family-names: Hériché
given-names: Jean-Karim
- family-names: Iudin
given-names: Andrii
- family-names: Martins
given-names: Gabriel G.
- family-names: Meehan
given-names: Terry
- family-names: Narayan
given-names: Kedar
- family-names: Patwardhan
given-names: Ardan
- family-names: Russell
given-names: Matthew Robert Geoffrey
- family-names: Saibil
given-names: Helen R.
- family-names: Strambio-De-Castillia
given-names: Caterina
- family-names: Swedlow
given-names: Jason R.
- family-names: Tischer
given-names: Christian
- family-names: Uhlmann
given-names: Virginie
- family-names: Verkade
given-names: Paul
- family-names: Barlow
given-names: Mary
- family-names: Bayraktar
given-names: Omer
- family-names: Birney
given-names: Ewan
- family-names: Catavitello
given-names: Cesare
- family-names: Cawthorne
given-names: Christopher
- family-names: Wagner-Conrad
given-names: Stephan
- family-names: Duke
given-names: Elizabeth
- family-names: Paul-Gilloteaux
given-names: Perrine
- family-names: Gustin
given-names: Emmanuel
- family-names: Harkiolaki
given-names: Maria
- family-names: Kankaanpää
given-names: Pasi
- family-names: Lemberger
given-names: Thomas
- family-names: McEntyre
given-names: Jo
- family-names: Moore
given-names: Josh
- family-names: Nicholls
given-names: Andrew W.
- family-names: Onami
given-names: Shuichi
- family-names: Parkinson
given-names: Helen
- family-names: Parsons
given-names: Maddy
- family-names: Romanchikova
given-names: Marina
- family-names: Sofroniew
given-names: Nicholas
- family-names: Swoger
given-names: Jim
- family-names: Utz
given-names: Nadine
- family-names: Voortman
given-names: Lenard M.
- family-names: Wong
given-names: Frances
- family-names: Zhang
given-names: Peijun
- family-names: Kleywegt
given-names: Gerard J.
- family-names: Brazma
given-names: Alvis
date-published: "2021-05-21"
doi: 10.1038/s41592
end: 1422
issue: 12
journal: Nature Methods
scope: "Used for the 'REMBI - Mapping' part. Templates from CAi were based on this publication as well as filling one of these templates on site and conceptual discussions on mapping touched the publication's content."
start: 1418
title: "REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology"
type: article
url: "https://doi.org/10.1038/s41592-021-01166-8"
volume: 18
year: 2021
- authors:
- affiliation: German Cancer Research Center
family-names: Schmidt
given-names: Christian
orcid: 0000-0001-9568-895X
- affiliation: German Cancer Research Center
family-names: Bortolomeazzi
given-names: Michele
orcid: 0000-0001-5805-5774
- affiliation: "Heinrich Heine University Düsseldorf"
family-names: Boissonnet
given-names: Tom
orcid: 0000-0002-3328-9467
- affiliation: "Max Planck Institute for Evolutionary Biology, Plön, Germany"
family-names: Fortmann-Grote
given-names: Carsten
orcid: 0000-0002-2579-5546
- affiliation: "Osnabrück University"
family-names: Dohle
given-names: Julia
- affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases
family-names: Zentis
given-names: Peter
orcid: 0000-0002-6999-132X
- affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases
family-names: Kandpal
given-names: Niraj
orcid: 0009-0007-5101-4786
- affiliation: "Osnabrück University"
family-names: Kunis
given-names: Susanne
orcid: 0000-0001-6523-7496
- affiliation: "University of Münster"
family-names: Zobel
given-names: Thomas
orcid: 0000-0002-2101-8416
- affiliation: "Heinrich Heine University Düsseldorf"
family-names: Weidtkamp-Peters
given-names: Stefanie
orcid: 0000-0001-7734-3771
- affiliation: German Cancer Research Center
family-names: Ferrando-May
given-names: Elisa
orcid: 0000-0002-5567-8690
date-released: "2023-11-13"
doi: 10.5281/zenodo.8323588
keywords:
- OMERO
- Open educational resources
- Data management
- Microscopy
- Bioimaging
- Ontologies
- Fiji
- Training
- teaching-learning material
- instructional material
- teaching aid
license: CC-BY-4.0
publisher: Zenodo
title: "I3D:bio's OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training"
type: generic
year: 2023
- authors:
- affiliation: Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
family-names: Schrader
given-names: Andrea
orcid: 0000-0002-3879-7057
date-released: "2024-01-09"
doi: 10.5281/zenodo.10475430
keywords:
- doi