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
Comprehensive pipeline for cell segmentation, tracking, and correlation analysis in time-lapse microscopy data. Utilizes deep learning models (Cellpose) for segmentation, with integrated refinement, tracking, and correlation analysis of dynamic cellular behaviors. Developed as part of a Master’s thesis project at KTH Royal Institute of Technology.
Mammary cell shape computation over time with Trackmate-Cellpose
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/
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
Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.
End-to-end pipeline for spinal-cord microscopy segmentation with Cellpose, tiling, and mask stitching.
Python Instance (map) Eikonal Function Solver
Segmentation of microscopy images and data analysis pipeline with a graphical user interface, powered by Cellpose.
Open Call #1: Segmentation and Tracking of Epithelial Cells
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
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