This repository provides StarDist and CellPose models, meticulously trained on a large dataset of Pancreatic Ductal Adenocarcinoma organoids co-cultured with immune cells. Pre-print available at https://www.biorxiv.org/content/10.1101/2024.02.12.580032v1. Demo application available at https://segmentorganoids.streamlit.app/
Pipeline meant to segment and classify organoids, or any other blob-like structures (star-convex polygons). Microscopy images can be easily annotated in QuPath and automatically processed afterwards to count the class distribution within each image using this pipeline (TIF files will be converted to grayscale)
pipeline for fast semantic segmentation of microscopy images of 3D cell cultures
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