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

Wrapper code for segmentation of cells and nuclei with Cellpose.

Python Instance (map) Eikonal Function Solver

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.

a wrapper for cellpose: contains spagetti

Open Call #1: Murine Skeletal Muscle Analysis

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/

Encoder-Decoder Cell and Nuclei segmentation models

Open Call #1: Segmentation and Tracking of Epithelial Cells

Large-scale cell segmentation with cellpose.

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