Cell Segmentation Python Packages

cellpose

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

116K 2K 649

stardist

StarDist - Object Detection with Star-convex Shapes

33K 1K 283

ncolor

Fast 4-coloring of instance segmentation label images (N-color relabeling) for Python, C++ core

12K 16 2

tiatoolbox

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

3K 557 113

lazyslide

Accessible and interoperable whole slide image analysis for digital pathology in Python

2K 328 32

micro-sam

Segment Anything for Microscopy

2K 735 113

cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

1K 108 5

napari-tmidas

Automated batch processing of cell and tissue microscopy image data in Napari

1K 23 1

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

1K 3 0

omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation

973 165 46

spateo-release

Spatiotemporal modeling of spatial transcriptomics

724 344 45

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, MICCAI'26]

594 263 90

cellcoloc

A Python package for interactive, segmentation-based colocalization analysis in microscopy images

473 1 0

yeastvision

Deep-learning enabled quantitative image analysis of cell full lifecycles

473 4 2

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

424 9 1

stardist-napari

StarDist plugin for napari

337 42 10

suite2p-haisslab

cell detection in calcium imaging recordings

331 2 1

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.

319 79 20

cellpose-vollseg

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

189 2K 649

macsima-qc

Quality control pipeline for MACSima / MACSiQView cell segmentation

184 1 0

vitaminp

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

135 13 2

kartezio

Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming

124 40 6

cellsepi

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

90 1 1

omnipose-acdc

Omnipose: a high-precision solution for morphology-independent cell segmentation

87 165 46