Encoder-Decoder Cell and Nuclei segmentation models
Large-scale cell segmentation with cellpose.
Graphical tool for creating image segmentation annotations and training custom Cellpose models
Wrapper code for segmentation of cells and nuclei with Cellpose.
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/
Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.
Python Instance (map) Eikonal Function Solver
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
Mammary cell shape computation over time with Trackmate-Cellpose
Open Call #1: Murine Skeletal Muscle Analysis
A snakemake pipeline to perform cell segmentation on MERFISH spatial transcriptomics data.
Single cell resolution 3D imaging and segmentation within intact live tissues
Open Call #1: Segmentation and Tracking of Epithelial Cells
Cell segmentation and tracking pipeline for time-lapse microscopy data using Cellpose. Includes segmentation, tracking, and correlation analysis of cell properties over time.
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