Organotchi: an open-source tool for the automated segmentation, morphological characterization, and longitudinal tracking of organoids

Organotchi is an open-source tool that automates neural organoid segmentation and longitudinal tracking, quantifying ten morphological features and flagging outliers and segmentation failures.

• Why it matters: Existing brightfield-based organoid tools often require manual or ad hoc steps for morphology characterization, quality assessment, and condition comparisons, limiting objective longitudinal analysis.
• What they did: Organotchi integrates automated segmentation with longitudinal morphological analysis, quantifying ten features (e.g., area, perimeter, eccentricity), tracking cystic structures over time, and reporting within- and between-batch variability.
• The result: Applied as a proof of concept, it supports disease modeling, pharmacological perturbation, and protocol optimization in neural organoids, and it assesses drug response in breast cancer spheroids.

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