Fractal: Towards FAIR bioimage analysis at scale with OME-Zarr-native workflows

Lüthi, J.; Cerrone, L.; Comparin, T.; Hess, M.; Hornbachner, R.; Tschan, A.; Glasner de Medeiros, G. Q.; Repina, N. A.; Cantoni, L. K.; Steffen, F. D.; Bourquin, J.-P.; Liberali, P.; Pelkmans, L.; Uhlmann, V.

doi:10.64898/2026.03.05.709921

bioRxiv · 10.64898/2026.03.05.709921

Fractal: Towards FAIR bioimage analysis at scale with OME-Zarr-native workflows

Lüthi, J.·Cerrone, L.·Comparin, T.·Hess, M.·Hornbachner, R.·Tschan, A.·Glasner de Medeiros, G. Q.·Repina, N. A.·Cantoni, L. K.·Steffen, F. D.·Bourquin, J.-P.·Liberali, P.·Pelkmans, L.·Uhlmann, V.

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Abstract

The rapid growth in microscopy data volume, dimensionality, and diversity urgently calls for scalable and reproducible analysis frameworks. While efforts on the open OME-Zarr format have helped standardize the storage of large microscopy datasets, solutions for standardized processing are still lacking. Here, we introduce two complementary contributions to address this gap: 1) the Fractal task specification, defining OME-Zarr processing units that can interoperate across computational environments and workflow engines, and 2) the Fractal platform, using this specification to enable scalable and modular OME-Zarr-native analysis workflows. We demonstrate their use across diverse biological research data, including terabyte-scale multiplexed, volumetric, and time-lapse imaging. In a clinical setting, we show that Fractal workflows achieve near-identical quantification of millions of cells across independent deployments, demonstrating the reproducibility required for translational applications. With its growing community of contributors, the Fractal ecosystem provides a foundation for FAIR microscopy image analysis relying on open file formats.

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Lüthi, J., Cerrone, L., Comparin, T., Hess, M., Hornbachner, R., Tschan, A., Glasner de Medeiros, G. Q., Repina, N. A., Cantoni, L. K., Steffen, F. D., Bourquin, J.-P., Liberali, P., Pelkmans, L., Uhlmann, V.. 2026-03-09. Fractal: Towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. https://doi.org/10.64898/2026.03.05.709921

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