Cell Segmentation Python Packages

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

stardist

StarDist - Object Detection with Star-convex Shapes

tiatoolbox

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

yeastvision

Deep-learning enabled quantitative image analysis of cell full lifecycles

napari-tmidas

A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues

deepliif

DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification

cellsepi

Segmentation of microscopy images and data analysis pipeline with a graphical user interface, powered by Cellpose.

stardist-napari

StarDist plugin for napari

vitaminp

VitaminP: a vision transformer-assisted multimodal integration network for pathology cell segmentation

u-segment3d

Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

suite2p-haisslab

cell detection in calcium imaging recordings

spateo-release

Spatiotemporal modeling of spatial transcriptomics

napari-nuclephaser

A Napari plugin to detect and count nuclei on phase contrast images

cellpose-vollseg

modification of cellpose algorithm

kartezio

Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming

fluospotter

Fluospotter is an end-to-end pipeline designed for nuclei segmentation and puncta detection in fluorescence microscopy images.

seg2link

A napari based 3D segmentation software for electron microscopy images

scellseg

A style-aware deep learning model for adaptive cell instance segmentation by contrastive fine-tuning.