ViTAMIn-O: Democratizing computer vision-based machine learning for stem cell research

Authors

Hamurcu, F., Breunig, M., Varga, A., Bosch, B., Lindenmayer, J., Kanakapaddy, A. T., Achberger, K., Pashkovskaia, N., Kleger, A., Liebau, S., Klingenstein, S., Klingenstein, M.

Abstract

Deep Learning (DL) holds exciting potential in automating the prediction of organoid differentiation results. Nevertheless, current models lack adaptability, openness, and robustness in performance. Additionally, broad employments of predictive models in wet-lab settings necessitate machine learning expertise, often not readily available in biologically oriented laboratories. To offer an intuitive solution, we present ColabViTAMIn-O, a code-free platform together with ViTAMIn-O. ViTAMIn-O is a fully open organoid-specific DL model trained and tested on a total of 34 organoid categories, incorporating annotated images across transmitted light microscopy (TLM) modalities at single-organoid resolution. It is adaptable to downstream prediction tasks of varying dataset sizes and outperforms established models even with linear-probing. It performs reliably within a few-shot framework and is even extensible to human embryo TLM imaging data at single specimen level. By releasing our platform, centralized model hub, and datasets, we hope to encourage broader deployments of specialized DL models in stem-cell laboratories.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 04 Jun 2026.

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