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MouseLand
cellpose

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

85K 2K 610
vanvalenlab
deepcell

Deep Learning Library for Single Cell Analysis

3K 474 107
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
vanvalenlab
deepcell-cpu

Deep Learning Library for Single Cell Analysis

1K 474 107
Sentinal4D
cellshape

3D shape analysis using deep learning

1K 31 6
DanuserLab
u-unwrap

Map complex and diverse 2D cell shapes into canonical disk and rectangular coordinate systems for streamlined analysis including spatiotemporal registration, windowing and machine learning. Also supports 2D contour-guided remapping and windowing. 2D analogous package to our 3D version, u-Unwrap3D.

819 0 0
Pablo1990
pyvertexmodel

3D vertex model allowing scutoids

697 3 0
epitools
epitools

Quantifying 2D cell shape and epithelial tissue dynamics

629 9 1
deweylab
cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

613 68 14
PraiseTheDarkFlo
cellsepi

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

595 1 0
AllenCellModeling
actk

Automated Cell Toolkit

555 24 4
tumoroids
spheroidpy

Python Package for the Analysis of Spheroid Microcopy Data

500 4 0
pablo1990
napari-pyvertexmodel

Napari plugin to run 3D vertex model

481 1 0
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.

394 68 12
vanvalenlab
deepcelltl

Deep Learning Library for Single Cell Analysis

321 474 107
surajinacademia
cellpose-mcp

MCP server for AI-powered Cellpose cell segmentation via Model Context Protocol

288 0 0
biosimulations
biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

267 1 0
biosimulators
biosimulators-rbapy

BioSimulators-compliant command-line interface to the RBApy simulation program.

227 0 0
MouseLand
cellpose-vollseg

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

193 2K 610
bioshape-lab
cellgeometry

A web-based application for Cell Shape Analysis.

169 2 0
DanuserLab
u-unwrap3d

Surface-guided computing of arbitrary 3D surfaces and volumes by bidirectional mapping to lower dimensions

140 36 4
sacha-ichbiah
optiflow

Reconstruction of flows from kymographs with optimal transport

128 4 0
alexisjapas
napari-vesicles-segmentation

A simple plugin to detect vesicles in cells images.

110 5 0
arnaublanco
fluospotter

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

109 3 0
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