preprints_ui: 5uhwz_v2
Data license: ODbL (database) & original licenses (content) · Data source: Open Science Framework
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| 5uhwz_v2 | 2024 OME-NGFF workflows hackathon | The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter at the University of Zurich, brought together an international group of researchers and developers to develop the ecosystem around the open, scalable, and FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing the OME-Zarr specification, (2) enabling workflow interoperability by integrating OME-Zarr image processing tasks across multiple open-source frameworks, (3) expanding Java support for Zarr v3 and enhancing the compatibility of OME-Zarr with the popular bioimage analysis software Fiji, and (4) improving the Python resources supporting OME-Zarr. The event led to the release of OME-Zarr 0.5, which formalizes the adoption of Zarr v3 and introduces a sharding strategy to reduce file system overhead. This report provides an overview of the key discussions, outcomes, and future directions emerging from the hackathon, with the goal of fostering continued community engagement in developing OME-Zarr as a robust open bioimaging standard. | 2025-03-13T15:52:29.933088 | 2025-03-14T02:14:21.772524 | 2025-03-14T02:12:05.532132 | biohackrxiv | 1 | accepted | 2 | 1 | https://doi.org/10.37044/osf.io/5uhwz_v2 | CC-By Attribution 4.0 International | FAIR; NGFF; bioimaging; ome-zarr; workflows; zarr | ["FAIR", "NGFF", "bioimaging", "ome-zarr", "workflows", "zarr"] | Joel Lüthi; Marvin Albert; Liviu Anita; Kola Babalola; Davis Bennett; John A. Bogovic; Lorenzo Cerrone; Rémy Dornier; Jan Eglinger; Vera Galinova | [{"id": "6nsp3", "name": "Joel L\u00fcthi", "index": 0, "orcid": "0000-0003-3023-170X", "bibliographic": true}, {"id": "9dcq2", "name": "Marvin Albert", "index": 1, "orcid": null, "bibliographic": true}, {"id": "jgc8p", "name": "Liviu Anita", "index": 2, "orcid": null, "bibliographic": true}, {"id": "ewrts", "name": "Kola Babalola", "index": 3, "orcid": null, "bibliographic": true}, {"id": "s9x6d", "name": "Davis Bennett", "index": 4, "orcid": null, "bibliographic": true}, {"id": "5sy2w", "name": "John A. Bogovic", "index": 5, "orcid": null, "bibliographic": true}, {"id": "b4u5r", "name": "Lorenzo Cerrone", "index": 6, "orcid": null, "bibliographic": true}, {"id": "p64na", "name": "R\u00e9my Dornier", "index": 7, "orcid": null, "bibliographic": true}, {"id": "4weu2", "name": "Jan Eglinger", "index": 8, "orcid": "0000-0001-7234-1435", "bibliographic": true}, {"id": "6hxf7", "name": "Vera Galinova", "index": 9, "orcid": null, "bibliographic": true}] | Joel Lüthi | Physical Sciences and Mathematics; Life Sciences; Bioinformatics; Biology; Computer Sciences; Research Methods in Life Sciences | [{"id": "66defcee6c7cdc67bcf54ead", "text": "Physical Sciences and Mathematics"}, {"id": "66defcee6c7cdc67bcf54eb0", "text": "Life Sciences"}, {"id": "66defcf46c7cdc67bcf54ef3", "text": "Bioinformatics"}, {"id": "66defd0b6c7cdc67bcf55002", "text": "Biology"}, {"id": "66defd146c7cdc67bcf5508e", "text": "Computer Sciences"}, {"id": "66defd266c7cdc67bcf551ba", "text": "Research Methods in Life Sciences"}] | https://osf.io/download/67d2ff4d86f2525b5800f0b1 | 1 | Many of the authors have been involved with the development of the OME-Zarr specification and tools in its ecosystem already before the hackathon. Norman Rzepka and Hannes Spitz are affiliated with scalable minds, a company that builds, delivers, supports and integrates image analysis solutions. Norman Rzepka owns equity in scalable minds. Matthew McCormick is the President of the Insight Software Consortium, a NumFOCUS fiscally sponsored project that support the Insight Toolkit (ITK), a toolkit used in the OME-Zarr community, and currently works at Fideus Labs, which provides professional scientific software services including support for the OME-Zarr ecosystem. Szymon Stoma and Filip Mroz are affiliated with Histopixel, a software house specializing in bioimage analysis. Szymon Stoma owns equity in Histopixel. Maximilian Schulz works as a research software engineer at the Institute of Human Biology (IHB) as part of Roche’s Pharma Research and Early Development (pRED). Eric Perlman is the principal of Yikes LLC, a consultancy providing data management support to individual labs in the life science, including the use of OME-Zarr as a key component. | available | not_applicable | [] | 2025-04-09T21:06:19.330460 |