The following resources and references were essential for creating this collection:

• EMBL — Europe’s intergovernmental life-science laboratory, combining research, scientific services, training and sites across Europe https://www.embl.org/ 
• EMBL-EBI — EMBL’s European Bioinformatics Institute, providing major biological data resources, tools, research and training https://www.ebi.ac.uk/ 
• STANDFLOW — EMBL Planetary Biology project developing standardised workflows for FAIR bioimage data management and sharing https://www.embl.org/about/info/planetary-biology/projects/standflow/ 
• TREC European Network — EMBL’s “Traversing European Coastlines” network for studying coastal ecosystems across Europe https://www.embl.org/about/info/trec/european-network/ 
• EMBL Planetary Biology — EMBL programme connecting molecular biology with ecosystems, environmental change and life in natural contexts. https://www.embl.org/about/info/planetary-biology/ 
• Université Grenoble Alpes — French research-intensive university with a large student body and many laboratories across Grenoble and the Alps region https://www.univ-grenoble-alpes.fr/english/home-628540.kjsp 
• CEA — French technological research organisation working across energy, digital technologies, health, defence and scientific innovation https://www.cea.fr/english/Pages/Welcome.aspx 
• GerBI-GMB — German BioImaging network supporting microscopy, bioimage analysis, imaging core facilities and research data management https://gerbi-gmb.de/ 
• NFDI4BIOIMAGE — German consortium providing guidance, tools and training for research data management in bioimaging and bioimage analysis https://nfdi4bioimage.de/home/ 
• Euro-BioImaging — European research infrastructure offering open access to biological and biomedical imaging technologies, expertise and data services https://www.eurobioimaging.eu/ 
• EMBRC — European Marine Biology Resource Centre consortium of marine stations, data services and biodiversity networks https://www.embrc.eu/
• Open Microscopy Environment — Consortium developing open microscopy software and standards such as OMERO, Bio-Formats and OME-Zarr/NGFF https://www.openmicroscopy.org/ 
• Global BioImaging — International network connecting imaging infrastructures worldwide through cooperation, training and capacity building https://globalbioimaging.org/ 
• RDMkit — ELIXIR toolkit offering best-practice guidance for life-science research data management and FAIR data https://rdmkit.elixir-europe.org/ 
• NEUBIAS training resources — Collection of training modules to understand basic principles of image data and the usage of bioimage-analysis tools: https://neubias.github.io/training-resources/
• Image.sc — Community forum for scientific image analysis, microscopy software, bioimage informatics and related troubleshooting http://Image.sc 
• VolumeEM — Community network focused on volume electron microscopy for visualising biological ultrastructure in 3D https://www.volumeem.org/ 
• EMBL vEM course — EMBL course on volume electron microscopy by automated serial scanning electron microscopy https://www.embl.org/about/info/course-and-conference-office/events/vem25-01/ 
• “How to organise and share my imaging data?” — EMBL-EBI/STANDFLOW training event on practical bioimaging data organisation and sharing https://www.ebi.ac.uk/training/events/how-organise-and-share-my-imaging-data/ 
• Euro-BioImaging FAIR Data Services — Services, templates, guidance and training to help make image data FAIR https://www.eurobioimaging.eu/image-data-services/fair-data-services/ 
• Research Data Alliance — Global community developing recommendations, working groups and practices for data sharing and interoperability https://www.rd-alliance.org/ 
• FAIR Guiding Principles paper — Foundational paper defining FAIR data as findable, accessible, interoperable and reusable, especially for machine actionability https://www.nature.com/articles/sdata201618 
• Stanford Encyclopedia: Scientific Method — Philosophical overview of scientific method, emphasising its diversity and historical complexity https://plato.stanford.edu/entries/scientific-method/ 
• European Commission, Cost-Benefit analysis for FAIR research data – Cost of not having FAIR research data, 2018, https://op.europa.eu/en/publication-detail/-/publication/d375368c-1a0a-11e9-8d04-01aa75ed71a1 
• Creative Commons licenses — Standard open licences that define how creative and research outputs can be reused, attributed and shared https://creativecommons.org/licenses/ 
• LabID user docs — Documentation for EMBL’s Lab Integrated Data platform covering ELN, inventory, protocols, samples, datasets and metadata: https://grp-gbcs.embl-community.io/labid-user-docs
• EuBI-Bridge — Distributed workflow/tool for converting microscopy image collections into OME-Zarr/NGFF https://euro-bioimaging.github.io/EuBI-Bridge/ 
• WEBKNOSSOS CLI convert — Documentation for converting image stacks into WEBKNOSSOS datasets for large-scale visualisation and annotation https://docs.webknossos.org/cli/convert.html 
• Vizarr — Lightweight web viewer for Zarr-based image data, built for interactive visualisation of large microscopy datasets https://github.com/hms-dbmi/vizarr 
• Vol-E — Allen Cell online tool for visualising and exploring multi-channel 3D microscopy data, including OME-Zarr data https://vol-e.allencell.org/ 
• Neuroglancer — WebGL-based viewer for large volumetric datasets, widely used in connectomics and neuroscience https://connectomics.readthedocs.io/en/latest/external/neuroglancer.html 
• BigDataViewer — Fiji/ImageJ plugin for browsing and visualising very large multi-view image datasets https://imagej.net/plugins/bdv/ 
• MoBIE — Fiji-based tool for exploring large multimodal image datasets together with tables and annotations https://mobie.github.io/ 
• BioFile Finder — Allen Institute web application for searching, accessing, sharing and previewing scientific datasets using metadata https://bff.allencell.org/ 
• EcoTaxa — Platform for taxonomic classification and ecological annotation of plankton and other environmental images https://ecotaxa.obs-vlfr.fr/ 
• Nextflow — Workflow engine for scalable, reproducible and portable scientific pipelines across local, HPC and cloud environments https://www.nextflow.io/ 
• Snakemake — Workflow management system for reproducible data analysis using rule-based dependencies, containers and scalable execution https://snakemake.github.io/ 
• UseGalaxy — Public Galaxy server providing browser-based access to reproducible life-science data analysis workflows https://usegalaxy.org/ 
• WorkflowHub — FAIR registry for sharing, describing and publishing scientific computational workflows https://workflowhub.eu/ 
• GitHub — Developer platform for hosting code, collaborating on software projects, version control and automation https://github.com/ 
• MIT License — Permissive open-source software licence allowing reuse, modification and distribution with copyright notice preservation https://en.wikipedia.org/wiki/MIT_License 
• OME-NGFF — Next-generation bioimaging file format specification, including OME-Zarr for scalable, cloud-friendly image data https://ngff.openmicroscopy.org/ 
• EMPIAR-10310 gallery — Example BioImage Archive/EMPIAR dataset view for a FIB-SEM image dataset of Platynereis dumerilii https://www.ebi.ac.uk/bioimage-archive/galleries/EMPIAR-10310/IM1.html 
• Euro-BioImaging NGFF workshop — Training workshop on converting, validating, opening and visualising OME-Zarr/NGFF image data https://euro-bioimaging.github.io/ngff_workshop/ 
• Amazon S3 — Cloud object-storage service commonly used for scalable storage of large datasets, data lakes and web-accessible objects https://aws.amazon.com/s3/ 
• FAIRsharing — Curated registry of research data standards, databases, repositories and data policies https://fairsharing.org/ 
• PANGAEA — Data publisher and repository for georeferenced earth-system and environmental research data https://www.pangaea.de/ 
• OBIS — Ocean Biodiversity Information System, aggregating global marine species observation and biodiversity data https://obis.org/ 
• SEANOE — Open repository and publisher for marine research data, supporting DOI-based citation and long-term access https://www.seanoe.org/ 
• BioSamples — EMBL-EBI database linking biological sample descriptions to derived datasets and submissions https://www.ebi.ac.uk/biosamples/ 
• Roscoff Culture Collection — Marine culture collection distributing macroalgae, protists, bacteria and viruses from Roscoff: https://roscoff-culture-collection.org/
• protocols.io — Platform for creating, sharing, versioning and publishing experimental protocols http://protocols.io 
• Zenodo — General-purpose open research repository hosted by CERN/OpenAIRE that assigns DOIs to deposited outputs https://zenodo.org/ 
• SSBD repository — RIKEN repository for quantitative biological dynamics data and bioimaging datasets https://ssbd.riken.jp/repository/ 
• REMBI paper — Nature Methods paper introducing Recommended Metadata for Biological Images to improve image-data reuse and archiving https://doi.org/10.1038/s41592-021-01166-8 
• BioImage.IO — Community-driven model zoo for sharing standardised AI models for bioimage analysis http://bioimage.io 
• OLS4 — EMBL-EBI Ontology Lookup Service, providing access, search and APIs for biomedical ontologies https://www.ebi.ac.uk/ols4/ 
• BioPortal — NCBO repository for browsing, searching and using biomedical ontologies https://bioportal.bioontology.org/ 
• T4FS_0000441 — Terms4FAIRskills ontology term for the “principal investigator” role in FAIR/data-stewardship contexts http://purl.obolibrary.org/obo/T4FS_0000441 
• T4FS_0000105 — Terms4FAIRskills ontology term for the “project manager” role http://purl.obolibrary.org/obo/T4FS_0000105 
• T4FS_0000297 — Terms4FAIRskills ontology term for “research data management,” covering storage, access and preservation of research data http://purl.obolibrary.org/obo/T4FS_0000297 
• CRO_0000048 — Contributor Role Ontology term for a “hardware role,” relating to responsibility for computer hardware http://purl.obolibrary.org/obo/CRO_0000048 
• CRO_0000097 — Contributor Role Ontology term for a “funding source role,” covering provision of financial support http://purl.obolibrary.org/obo/CRO_0000097 
• CRO_0000093 — Contributor Role Ontology term for a “specimen collection role,” describing contribution to specimen/sample collection http://purl.obolibrary.org/obo/CRO_0000093 
• CRO_0000036 — Contributor Role Ontology term for a “data collection role,” covering collection of data for a project http://purl.obolibrary.org/obo/CRO_0000036 
• CRO_0000072 — Contributor Role Ontology term for a “data transformation role,” covering conversion or transformation of data http://purl.obolibrary.org/obo/CRO_0000072 
• CREDIT_00000005 — CRediT taxonomy term for the “investigation” role, including experiments and data/evidence collection http://purl.org/credit/ontology#CREDIT_00000005 
• CREDIT_00000002 — CRediT taxonomy term for the “data curation” role, covering data management and preparation for reuse http://purl.org/credit/ontology#CREDIT_00000002 
• T4FS_0000178 — Terms4FAIRskills ontology term for “data steward,” a support role for FAIR research data http://purl.obolibrary.org/obo/T4FS_0000178 
• CRO_0000069 — Contributor Role Ontology term for a “digital preservation role,” covering long-term preservation of digital resources http://purl.obolibrary.org/obo/CRO_0000069 
• PCO_0000035 — Population and Community Ontology term “party,” defined as a type of human social gathering http://purl.obolibrary.org/obo/PCO_0000035 
• CRO_0000016 — Contributor Role Ontology term for an “education and training role,” covering teaching or training contributions http://purl.obolibrary.org/obo/CRO_0000016 
• Zenodo record 13945179 — “Image Repository Decision Tree,” a guide for choosing where to deposit imaging data https://zenodo.org/records/13945179 
• Falk zarr illustrations — Zenodo record for reusable Zarr illustrations by Henning Falk, created for explaining Zarr concepts – Falk, H. zarr-developers/zarr-illustrations-falk-2022 | Zenodo [WWW Document], 2022. URL https://doi.org/10.5281/zenodo.7037367 (accessed 26.02.2022).