BioImage Model Zoo — FAIR AI Models for Microscopy

The BioImage Model Zoo is a community-driven, fully open resource where standardized, pre-trained deep-learning models can be shared, explored, tested directly in the browser, and deployed in many end-user tools — including ilastik, deepImageJ, QuPath, StarDist, ImJoy, and ZeroCostDL4Mic. A shared model standard makes these models cross-compatible, so a model contributed once can be reused everywhere.

The AICell Lab leads the user services and cloud infrastructure behind the Zoo: the model-upload and testing pipelines, and the BioEngine backend that runs the in-browser “test run” feature. Our goal is to make deep-learning methods for microscopy findable, accessible, interoperable, and reusable (FAIR) across the whole bioimaging ecosystem. This effort grew out of the now-completed AI4Life project and continues as a living community platform.

Recent additions push the Zoo further into the browser: in-browser model testing on cloud or HPC GPUs via BioEngine (no install, no local GPU); a collaborative annotation layer with AI-assisted segmentation (Cellpose and Cellpose-SAM); and an agent skill that lets any AI assistant guide a researcher through contributing a model end to end — packaging, validating, and submitting it. Much of this runs entirely client-side via Pyodide/WebAssembly, backed by Hypha Cloud.

Read more in our preprint.