Cell Biology Python Packages

cellpose

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

deepcell

Deep Learning Library for Single Cell Analysis

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]

deepcell-cpu

Deep Learning Library for Single Cell Analysis

cellshape

3D shape analysis using deep learning

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.

pyvertexmodel

3D vertex model allowing scutoids

cellsepi

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

cello-classify

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

actk

Automated Cell Toolkit

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

napari-pyvertexmodel

Napari plugin to run 3D vertex model

spheroidpy

Python Package for the Analysis of Spheroid Microcopy Data

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.

deepcelltl

Deep Learning Library for Single Cell Analysis

cellpose-mcp

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

biosimulations-bigg

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

biosimulators-rbapy

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

cellpose-vollseg

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

cellgeometry

A web-based application for Cell Shape Analysis.

u-unwrap3d

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

optiflow

Reconstruction of flows from kymographs with optimal transport

napari-vesicles-segmentation

A simple plugin to detect vesicles in cells images.

fluospotter

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