Cell Segmentation Python Packages

cellpose

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

104K 2K 637

stardist

StarDist - Object Detection with Star-convex Shapes

32K 1K 277

tiatoolbox

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

10K 537 106

cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

4K 103 6

micro-sam

Segment Anything for Microscopy

3K 697 105

cellcoloc

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

2K 0 0

macsima-qc

Quality control pipeline for MACSima / MACSiQView cell segmentation

2K 1 0

napari-tmidas

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

2K 20 1

cellsepi

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

1K 1 1

yeastvision

Deep-learning enabled quantitative image analysis of cell full lifecycles

1K 4 2

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]

1K 254 91

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

795 3 0

stardist-napari

StarDist plugin for napari

742 40 10

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

672 9 1

vitaminp

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

634 12 1

suite2p-haisslab

cell detection in calcium imaging recordings

620 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.

528 71 13