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Cell Segmentation Python Packages

Python packages with the GitHub topic cell-segmentation. Sorted by relevance, with stars and monthly downloads.
MouseLand
cellpose

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

87K 2K 610
stardist
stardist

StarDist - Object Detection with Star-convex Shapes

36K 1K 271
TissueImageAnalytics
tiatoolbox

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

33K 526 109
berkyalcinkaya
yeastvision

Deep-learning enabled quantitative image analysis of cell full lifecycles

2K 4 2
okunator
cellseg-models-pytorch

Encoder-Decoder Cell and Nuclei segmentation models

2K 100 5
nadeemlab
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]

2K 249 90
macromeer
napari-tmidas

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

2K 13 0
stardist
stardist-napari

Object Detection with Star-convex Shapes

797 39 10
PraiseTheDarkFlo
cellsepi

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

692 1 0
nikvo1
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

582 3 0
epitools
epitools

Quantifying 2D cell shape and epithelial tissue dynamics

547 9 1
JostTim
suite2p-haisslab

Pipeline for calcium imaging

546 2 1
idso-fa1-pathology
vitaminp

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

473 8 1
aristoteleo
spateo-release

Spatiotemporal modeling of spatial transcriptomics

454 337 43
DanuserLab
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.

423 68 12
KevinCortacero
kartezio

Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming

225 37 6
MouseLand
cellpose-vollseg

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

202 2K 610
arnaublanco
fluospotter

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

104 3 0
WenChentao
seg2link

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

66 6 1
cellimnet
scellseg

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

39 10 2
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