High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos.

ABSTRACT: Three-dimensional (3D) organoid cultures are flexible systems to interrogate cellular growth, morphology, multicellular spatial architecture, and cellular interactions in response to treatment. However, computational methods for analysis of 3D organoids with sufficiently high-throughput and cellular resolution are needed. Here we report Cellos, an accurate, high-throughput pipeline for 3D organoid segmentation using classical algorithms and nuclear segmentation using a trained Stardist-3D convolutional neural network. To evaluate Cellos, we analyze ~100,000 organoids with ~2.35 million cells from multiple treatment experiments. Cellos segments dye-stained or fluorescently-labeled nuclei and accurately distinguishes distinct labeled cell populations within organoids. Cellos can recapitulate

SUBMITTER: Mukashyaka P 

PROVIDER: S-EPMC10730814 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature