Publications

ZORA Publication List

Publications

• 2025

  • Journal Article

    • Zulueta-Coarasa, T., Jug, F., Mathur, A., Moore, J., Muñoz-Barrutia, A., Anita, L., Babalola, K., Bankhead, P., Paul-Gilloteaux, P., Gogoberidze, N., Jones, M. L., Kleywegt, G. J., Korir, P., Kreshuk, A., Küpcü Yoldaş, A., Marconato, L., Narayan, K., Norlin, N., Oezdemir, B., … Hartley, M. (2025). MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis Nature Methods, 22(11), 2245–2252. https://doi.org/10.1038/s41592-025-02835-8
    • Woodhams, B., & Uhlmann, V. (2025). From images to understanding: Advances in deep learning for cellular dynamics analysis Current Opinion in Cell Biology, 97, 102585. https://doi.org/10.1016/j.ceb.2025.102585
    • Russell, C. T., Burel, J.-M., Athar, A., Li, S., Sarkans, U., Swedlow, J., Brazma, A., Hartley, M., & Uhlmann, V. (2025). bia-binder: a web-native cloud compute service for the bioimage analysis community Bioinformatics, 41(8), btaf412. https://doi.org/10.1093/bioinformatics/btaf412

  • Working Paper

    • Lüthi, Joel; Marvin, Albert; Anita, Liviu; Babalola, Kola; Bennett, Davis; Bogovic, John A; Cerrone, Lorenzo; Dornier, Rémy; Eglinger, Jan; Galinova, Vera; Gerber, Reto; Gros, Oane; Hahmann, Stefan; Hess, Max; Hornbachner, Ruth; Horyslavets, Dmytro; Huxford, Rachael; Krentzel, Daniel; LI, Tong; Marconato, Luca; McCormick, Matthew; Moos, Franziska; Mroz, Filip; Özdemir, Bugra; Pavie, Benjamin; Perlman, Eric; Schulz, Maximilian; Schwarz, Leonardo; Spitz, Hannes M; Stansby, David; Steffen, Fabio D; Stoma, Szymon; Sturzenegger, Flurin; Wouter-Michiel, Vierdag; Windhager, Jonas; Yamauchi, Kevin A; Zubarev, Igor; Moore, Josh; Rzepka, Norman; Tischer, Christian; Ulman, Vladimir; Uhlmann, Virginie (2025). 2024 OME-NGFF workflows hackathon BioHackrXiv NA, University of Zurich.

• 2024

  • Journal Article

    • Uhlmann, Virginie; Hartley, Matthew; Moore, Josh; Weisbart, Erin; Zaritsky, Assaf (2024). Making the most of bioimaging data through interdisciplinary interactions Journal of Cell Science, 137(20):jcs262139.
    • Cimini, Beth A; Bankhead, Peter; D'Antuono, Rocco; Fazeli, Elnaz; Fernandez-Rodriguez, Julia; Fuster-Barceló, Caterina; Haase, Robert; Jambor, Helena Klara; Jones, Martin L; Jug, Florian; Klemm, Anna H; Kreshuk, Anna; Marcotti, Stefania; Martins, Gabriel G; McArdle, Sara; Miura, Kota; Muñoz-Barrutia, Arrate; Murphy, Laura C; Nelson, Michael S; Nørrelykke, Simon F; Paul-Gilloteaux, Perrine; Pengo, Thomas; Pylvänäinen, Joanna W; Pytowski, Lior; Ravera, Arianna; Reinke, Annika; Rekik, Yousr; Strambio-De-Castillia, Caterina; Thédié, Daniel; Uhlmann, Virginie; et al (2024). The crucial role of bioimage analysts in scientific research and publication Journal of Cell Science, 137(20):jcs262322.
    • Fabrèges, Dimitri; Corominas-Murtra, Bernat; Moghe, Prachiti; Kickuth, Alison; Ichikawa, Takafumi; Iwatani, Chizuru; Tsukiyama, Tomoyuki; Daniel, Nathalie; Gering, Julie; Stokkermans, Anniek; Wolny, Adrian; Kreshuk, Anna; Duranthon, Véronique; Uhlman, Virginie; Hannezo, Edouard; Hiiragi, Takashi (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis Science, 386(6718):eadh1145.