Open Call #1: Segmentation and Tracking of Epithelial Cells

Open Call #1: Murine Skeletal Muscle Analysis

Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.

A snakemake pipeline to perform cell segmentation on MERFISH spatial transcriptomics data.

Graphical tool for creating image segmentation annotations and training custom Cellpose models

a wrapper for cellpose: contains spagetti

Python Instance (map) Eikonal Function Solver

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/

MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications is an ImageJ/Fiji Plugin for automatic segmentation of nuclei and/or cells for quantifications in other channels including foci detection

Large-scale cell segmentation with cellpose.

Wrapper code for segmentation of cells and nuclei with Cellpose.

Encoder-Decoder Cell and Nuclei segmentation models