cellpose-segmentation

Large-scale cell segmentation with cellpose.

Tutorial for scaling-up image analysis with dask

A fully AI-based workflow to quantify fusion index of skeletal muscle cells

End-to-end pipeline for spinal-cord microscopy segmentation with Cellpose, tiling, and mask stitching.

Cell seeding efficiency measurement using customized Cellpose SAM (cellpose4) models. The goal is to classify cells into four categories and calculate cell properties (number, average brightness, and average area) for each frame

Segmentation and analysis pipeline for high-resolution whole tissue images.

A modular platform for end-to-end batch cell segmentation and quantification for microscopy images.

RoiEditor that can run as plugin for Fiji or as standalone Jython application

Open-source toolkit for skeletal muscle microscopy analysis. Fiber segmentation, fiber typing, myonuclear fusion index, and myotube surface quantification.

Image processing pipeline for multi-modal images

Julia wrapper for Cellpose v4 enabling high-performance biological image segmentation.

End-to-end pipeline for segmentation and quantitative analysis of fluorescence microscopy data to study phase separation

semi-automated postprocessing of cellpose segmented images

Image-analysis pipeline for high-resolution SEM images of S. mutans biofilms: Cellpose deep-learning cell segmentation, per-cell morphology and texture features, matrix texture maps, and statistical treatment comparison. Code for a paper under revision at Scientific Reports.

Automated cell counter from microscopy images and dead/alive classification