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.

yeastvision

Deep-learning enabled quantitative image analysis of cell full lifecycles

cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

deepliif

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

napari-tmidas

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

stardist-napari

Object Detection with Star-convex Shapes

cellsepi

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

napari-nuclephaser

A Napari plugin for automated cell nuclei detection, cell proliferation & population growth analysis, and single-cell tracking in brightfield and fluorescence microscopy images

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

suite2p-haisslab

Pipeline for calcium imaging

vitaminp

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

spateo-release

Spatiotemporal modeling of spatial transcriptomics

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.

kartezio

Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming

cellpose-vollseg

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

fluospotter

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

seg2link

Napari-based 3D cell segmentation software using machine learning predictions as inputs, especially for EM image stacks of brains

scellseg

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