OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics

SUMMARY Organoid model systems recapitulate key features of mammalian tissues and enable high throughput experiments. However, the impact of these experiments may be limited by manual, non-standardized, static, or qualitative phenotypic analysis. OrgDyn is an open-source and modular pipeline to quantify organoid shape dynamics using a combination of feature and model based approaches on time series of 2D organoid contour images. Our pipeline consists of i) geometrical and signal processing feature extraction, ii) dimensionality reduction to differentiate dynamical paths, iii) time series clustering to identify coherent groups of organoids, and iv) dynamical modeling using point distribution models to explain temporal shape variation. OrgDyn can characterize, cluster, and model differences among unique dynamical paths that define diverse final shapes, thus enabling quantitative analysis of the molecular basis of tissue development and disease. AVAILABILITY AND IMPLEMENTATION https://github.com/zakih/organoidDynamics (BSD 3-Clause License). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.