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Cell Biology Python Packages

Python packages with the GitHub topic cell-biology. 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
vanvalenlab
deepcell

Deep Learning Library for Single Cell Analysis

2K 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.

854 0 0
Pablo1990
pyvertexmodel

3D vertex model allowing scutoids

789 3 0
PraiseTheDarkFlo
cellsepi

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

692 1 0
deweylab
cello-classify

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

677 68 14
AllenCellModeling
actk

Automated Cell Toolkit

547 24 4
epitools
epitools

Quantifying 2D cell shape and epithelial tissue dynamics

547 9 1
pablo1990
napari-pyvertexmodel

Napari plugin to run 3D vertex model

520 1 0
tumoroids
spheroidpy

Python Package for the Analysis of Spheroid Microcopy Data

519 4 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.

423 68 12
vanvalenlab
deepcelltl

Deep Learning Library for Single Cell Analysis

320 474 107
surajinacademia
cellpose-mcp

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

304 0 0
biosimulations
biosimulations-bigg

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

279 1 0
biosimulators
biosimulators-rbapy

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

241 0 0
MouseLand
cellpose-vollseg

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

202 2K 610
bioshape-lab
cellgeometry

A web-based application for Cell Shape Analysis.

186 2 0
DanuserLab
u-unwrap3d

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

148 36 4
sacha-ichbiah
optiflow

Reconstruction of flows from kymographs with optimal transport

133 4 0
alexisjapas
napari-vesicles-segmentation

A simple plugin to detect vesicles in cells images.

124 5 0
arnaublanco
fluospotter

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

104 3 0
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