What is IIIF?

IIIF stands for Image Interoperability Framework. According to their website, “IIIF (pronounced triple eye eff) is a set of open standards for delivering high-quality, attributed digital objects online at scale.” It comes with an international community and is backed by cultural institutions. IIIF allows you to access high-quality images quickly and flexibly.

By connecting Galaxy to IIIF, researchers can directly browse IIIF resources and import images into their Galaxy history for further analysis.

Adding IIIF repositories to Galaxy

Please note: the Galaxy IIIF integration is currently only available on usegalaxy.eu.

Galaxy integrates IIIF through its File Sources (Remote Files) framework, enabling researchers to search, browse, and import images from remote IIIF repositories directly into an active Galaxy history without first downloading them locally.

Adding and Browsing your IIIF repository

Hands On: Add your IIIF manifest to Galaxy

1. In Galaxy, navigate to the top menu, click on your user name and then Preferences.
2. Select Manage your Repositories and click the Create button.
3. Scroll down and select IIIF Manifest.
4. Complete the configuration form:
   • Name: A descriptive title (e.g., Bodleian library).
   • If you want, you can add an optional description.
   • IIIF Manifest URL: The full base URL of the IIIF manifest (e.g., https://iiif.bodleian.ox.ac.uk/iiif/collection/top).
5. Click Create.

After saving, your new entry appears in My Repositories.

![My Repositories] /training-material/topics/galaxy-interface/tutorials/iiif/bodleian.png

Once you have added your IIIF Manifest, you can access its content and load images into your history for further processing.

Hands On: Importing Discovered Files into Your History

Once the connection to your IIIF manifest is established, navigating and uploading the files follows a standardised routine:

1. Open the Upload Data menu and click Choose from repository.
2. Select your newly configured IIIF source.
3. Browse or Search: You can navigate the hierarchical collections or use the dataset-name search filter.
4. Select Files: Once you find the correct folder, click into it, tick the checkbox next to the desired files and hit Select.
5. Execute Import: The selected items will populate the standard Galaxy upload queue. Click Start to run the import process.

Once the progress bar turns green, the files will appear in the right-hand history panel as standard Galaxy datasets, ready to be routed into any analytical tool or workflow.

Depending on your needs, you can crop or preprocess the uploaded images in Galaxy, segment them or use them with other tools, for example, for optical character recognition. Why not try adding your favourite IIIF images now?

You've Finished the Tutorial

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Key points

• With the IIIF integration in Galaxy, you can directly browse IIIF from within Galaxy, eliminating manual download cycles.

Frequently Asked Questions

• Topic FAQs
• Galaxy FAQs
• GTN Matrix Chat
• Galaxy Help Forum

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Citing this Tutorial

1. Daniela Schneider, Accessing IIIF from within Galaxy (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/iiif/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{galaxy-interface-iiif,
author = "Daniela Schneider",
	title = "Accessing IIIF from within Galaxy (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/iiif/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

de.KCD

MWK

de.NBI

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