OME-Zarr and Next-Generational File Formats (NGFF)

CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 1 and Next-Generational File Formats (NGFF) The future of microscopy file formats? Josh Moore German BioImaging e.V. CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 2 What problem does it solve? What is the future of OME-TIFF? Why OME-ZARR as a format? Where do you see the benefits for a vendor when incorporating such a format? Is the NGFF Converter not enough? CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 3 Why OME-ZARR as a format? What problem does it solve? What is the future of OME-TIFF? Where do you see the benefits for a vendor when incorporating such a format? Is the NGFF Converter not enough? CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 4 Where do you see the benefits for a vendor when incorporating such a format? Is the NGFF Converter not enough? Accessing images without download Images by @DrHenningFalk,! ©2022 @NumFOCUS is used under a CC-BY 4.0 license. Why OME-ZARR as a format? What problem does it solve? What is the future of OME-TIFF? CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 5 Where do you see the benefits for a vendor when incorporating such a format? Is the NGFF Converter not enough? Standardizing the access protocol Neuroglancer Jeremy Maitin-Shepard, Google MoBIE Plugin Christian Tischer, EMBL Heidelberg webKnossos Norman Rzepka, scalableminds Images by @DrHenningFalk,! ©2022 @NumFOCUS is used under a CC-BY 4.0 license. Why OME-ZARR as a format? What problem does it solve? What is the future of OME-TIFF? CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 6 Acknowledgments BE VIB Benjamin Pavie // CH Bern Ana Stojiljkovic BioVisionCenter Joel Lüthi, Lorenzo Cerrone, Virginie Uhlmann EPFL Rémy Dornier ETH Kevin Yamauchi, Leonardo Schwarz FMI Franziska Moos, Gustavo de Medeiros, Jan Eglinger, Prisca Liberali Zürich Fabio Steffen, Flurin Sturzenegger, Grégory Paul, Reto Gerber, Ruth Hornbachner // CZ MUNI Vladimír Ulman // DE EMBL Luca Marconato, Oane Gros, Oliver Stegle, Wouter-Michiel Vierdag, Christian Tischer Euro BioImaging Bugra Özdemir German BioImaging Josh Moore, Johannes Soltwedel, Tom Boissonnet Göttingen Constantin Pape Helmholtz München Fabian J. Theis, Giovanni Palla, Isaac Virshup TU Dresden Stefan Hahmann // FR France BioImaging Guillaume GAY Pasteur Daniel Krentzel, Marvin Albert // JP RIKEN Hiroya Itoga, Koji Kyoda, Shuichi Onami // SE Lund University Nils Norlin SciLifeLab Jonas Windhager, Wei Ouyang, Xavier Casas Moreno // UK Crick Joost de Folter, Kenneth Ho, Martin Jones Dundee David Gault, Dominik Lindner, Frances Wong, Jason R. Swedlow, Jean-Marie Burel, Khaled Mohamed, William Moore EBI Aybüke Küpcü Yoldaş, Aybuke Kupcu Yoldas, Francois Sherwood, Kolawole Babalola, Liviu Anita, Matthew Hartley Sanger Omer Bayraktar, Daniela Basurto-Lozada, Dave Horsfall, Muzlifah Haniffa, Tong Li UCL David Stansby // US Allen Daniel Toloudis, Eva M. Brown, Gabor Kovacs, Sean Meharry Broad Beth A. Cimini, Erin Weisbart CZI BioHub Jordão Bragantini, Loic A. Royer, Ahmet Can Solak, Lerlin Lange Dartmouth Yaroslav O. Halchenko HMS Ilan Gold, Mark S. Keller, Nils Gehlenborg, Trevor Manz ITK Matthew McCormick JAX Erick Ratamero, Kiya Govek, Peter Sobolewski Janelia John Bogovic, Konrad Rokicki, Mark Kittisopikul, Stephan Saalfeld, Tobias Pietzsch MIT Satrajit S. Ghosh NIH Hythem Sidky, Nathan Hotaling, Nicholas Schaub, Sameeul Samee Pittsburgh Alan M. Watson UMN Rachael Huxford // Company Glencoe Chris Allan, Erin E. Diel, Melissa Linkert, Sébastien Besson Google Jeremy Maitin-Shepard Roche Dominique Roux, Maximilian Schulz Yikes Eric Perlman scalableminds Albane le Tournoulx de la Villegeorges, Hannes Spitz, Norman Rzepka, Jonathan Striebel Zeiss Sebastian Rhode, Stephan Wagner-Conrad & Many more Christoph Engwer, Davis Bennett, Dmytro Horyslavets, Filip Mroz, Igor Zubarev, Szymon Stoma, Vera Galinova along with 90+ other members of the image.sc group: adamkglaser, aeisenbarth, amathur, Anatole_Chessel, andriy, AnthonyA, arturo.pimentel, avweigel, bene.schmid, berl, berombau, biehli, Bill_Katz, brainio, brossetti, bruno, camlloyd, carandraug, Caterina, cgohlke, Christopher_Steele, ctr26, darshats, DragaDoncila, dsudar, ehrenfeu, EliS, fercer, folterj, frauzufall, GenevieveBuckley, glyg, Gonzalo_Merino, g-sands, Gucki, guiwitz, haesleinhuepf, hanslovsky, heeler, ilan-gold, imagejan, jandilla, jbms, jfkotw, jkh1, jlacoste, jni, JorgeGtz, jqshenker, jstitlow, juliomateos, kabilar, k-dominik, ken.ho, kephale, Kevin_Kozlowski, Kimberly_Meechan, lassoan, LDeakin, Lee_Kamentsky, leoburgy, lguerard, lmurphy, manics, maree, mellertd, memphizz, MinaG, neissner, NicoKiaru, olatarkowska, Oumou_DHMINE, paulkorir, petebankhead, petermajer, Research_Associate, rohola, Sarah_Aufmkolk, schienstockd, schorb, sebherbert, sofroniewn, Steen, Stephen_Taylor, stick, sukunis, talley, tibuch, UlrikeBoehm, uqathom9, VolkerH, Wojtek Goscinski https://zarr.dev/adopters ESA* Consultants: CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 7 Slide provided by Norman Rzepka scalableminds GmbH CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 8 Where do you see the benefits for a vendor when incorporating such a format? Is the NGFF Converter not enough? Download / “Cloud” Repositories & Archives Standard access protocol Developer interest Why OME-ZARR as a format? What problem does it solve? What is the future of OME-TIFF? CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 9 Where do you see the benefits for a vendor when incorporating such a format? Is the NGFF Converter not enough? No deprecation plans. Community (developer) support is limited. Adobe owns TIFF license. Performance is limited. Meta/data structures are limited. Why OME-ZARR as a format? What problem does it solve? What is the future of OME-TIFF? CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 16 Value Cost CZI OME-Zarr • Open • Scalable • Standardized CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 17 Value Cost No standard Having a standard Implementation spectrum: … “Full adoption” Export Import Translation • Ownership • Velocity • Quality* • Development • User support • Bio-Formats dependency* • maintenance • User experience* • Stability* • Interoperability • Mandatory? • AI-readiness • Engagement with process • Risk of stalling • Depth & breadth of implementations* * User impact https://forum.image.sc/t/streaming-czi-files-not-openingproperly-using-bio-formats-in-qupath-and-imagej/112218 CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 18 18 https://zenodo.org/communities/bio-formats/ https://forum.image.sc/tag/bio-formats The Bio-Formats way Uninterpretable metadata OME-XML CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 19 19 https://zenodo.org/communities/bio-formats/ https://forum.image.sc/tag/bio-formats Rosetta stone Original format OME-Zarr conversion ✓Version ✓Open License ✓Documentation With thanks to Becker & Hickl, Leica, and PicoQuant representatives for the conversations at: Rosetta Stone, a modest proposal Before providing integrated export or using OME-Zarr natively, such datasets would enable an evaluation of data conversion. CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 20 Extensions •Allow organizations to add functionality without modifying the specification •Prevent naming collisions Roadmap to 1.0 +----------------------+ | zarr_format: 3 | | node_type: array | | shape: [1024, 1024] | | ... | | extensions: [ | | { | | name: "acme.offset-index", | must_understand: true, | configuration: { offset: [100, 200] } | } | | ] | +----------------------+ CC-BY Josh Moore | Presented to Zeiss, 2.July 2025 21 21 Final thoughts • Next steps / Further meetings • Timelines / Roadmaps • Decision making (Voting, Industry boards) • Thanks for your time! • Questions and comments in German or English welcome. Hosted by: