GitHub topics: cell-biology

Repositories

MouseLand/cellpose

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

Language: Python - Size: 114 MB - Last synced at: 3 days ago - Pushed at: 22 days ago - Stars: 1,779 - Forks: 502

DanuserLab/u-unwrap3D

Transform 3D cell surfaces into different representations including topographic maps, 3D spheres, and 2D images for doing optimized quantification, data analysis and machine learning.

Language: Jupyter Notebook - Size: 52.7 MB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 29 - Forks: 2

jak18015/lab-rats

Common cell biology calculations

Language: Python - Size: 193 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

cantinilab/scPRINT Fork of jkobject/scPRINT

single cell foundation model for Gene network inference and more

Language: Jupyter Notebook - Size: 931 MB - Last synced at: 5 days ago - Pushed at: 22 days ago - Stars: 92 - Forks: 16

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]

Language: Python - Size: 94.5 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 205 - Forks: 79

DanuserLab/Focal-Adhesion

This focal adhesion package is a software that tracks, segments, classifies and analyzes the time series of focal- and nascent adhesions in an adhesion time-lapse images.

Language: MATLAB - Size: 86.2 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 0

DanuserLab/u-integrate

Pipeline for inference of Granger-causal relations in molecular systems to study actin regulation in lamellipodia

Language: MATLAB - Size: 1.81 GB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 5 - Forks: 1

DanuserLab/cmeAnalysis

clathrin-mediated endocytosis analysis

Language: MATLAB - Size: 81.8 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 9 - Forks: 1

Multiple-particle tracking designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events

Language: MATLAB - Size: 79.2 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 50 - Forks: 22

DanuserLab/u-register

Analyze local cell edge motions (e.g. protrusion and retraction) and to locally sample intracellular fluorescence signals in 2D fluorescence microscopy data.

Language: MATLAB - Size: 77.9 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 6 - Forks: 1

msymeonides/Migrate3D

A Python package for analyzing XYZ positional data of moving objects over time

Language: Python - Size: 725 KB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 6 - Forks: 1

WCCMS-UTAustin/3DTFM

Heterogeneous hydrogel modulus estimation for 3D traction force microscopy

Language: Jupyter Notebook - Size: 18.6 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0

KarrLab/wc_kb

Tools for building databases of experimental data for constructing whole-cell models

Language: Python - Size: 94.8 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 4 - Forks: 5

Pablo1990/pyVertexModel

3D vertex model allowing scutoids

Language: Python - Size: 184 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 3 - Forks: 0

PraiseTheDarkFlo/CellSePi

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

Language: Python - Size: 46.6 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 0

osa-bot/cellpose_plus Fork of ITMO-MMRM-lab/cellpose_plus

A morphological analysis tool for feature extraction of stained cell images built over Cellpose

Size: 127 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

DanuserLab/u-probe

Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of the biosensor.

Language: MATLAB - Size: 79.3 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 7 - Forks: 1

Vic-dev175/BioBreakdown

Simple site explaining and describing various biology topics!

Size: 82 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

vanvalenlab/deepcell-tf

Deep Learning Library for Single Cell Analysis

Language: Python - Size: 341 MB - Last synced at: 30 days ago - Pushed at: 11 months ago - Stars: 457 - Forks: 104

nadeemlab/ImPartial

Interactive deep learning whole-cell segmentation and thresholding using partial annotations

Language: Jupyter Notebook - Size: 175 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 39 - Forks: 3

pskeshu/cathedral

Epistemic integration engine for cell biology research - connecting empirical observations to fundamental questions about life through multi-modal experimental data analysis

Size: 2.93 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

SilasBoyeNissen/Cluster-Assembly-Dynamics-Drive-Fidelity-of-Planar-Cell-Polarity-Polarization

"Cluster Assembly Dynamics Drive Fidelity of Planar Cell Polarity Polarization" published in bioRxiv (2025)

Language: MATLAB - Size: 2.57 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

Borda/kaggle_image-segm

Simple tooling for instance segmentation aiming at cell biology...

Language: Jupyter Notebook - Size: 3.03 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 10 - Forks: 2

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.

Language: MATLAB - Size: 78.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 5

Pablo1990/3D-deep-segmentation-protocol

Single cell resolution 3D imaging and segmentation within intact live tissues

Language: Jupyter Notebook - Size: 48.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

epitools/epitools

Quantifying 2D cell shape and epithelial tissue dynamics

Language: Python - Size: 115 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 7 - Forks: 0

sashielvagus/Preparing-Undergraduates-Through-Mentoring-towards-PHD-s-Project

Created two MATLAB codes using ROI and image-based processing to quantify the area of proliferation cells in three different types of tissues for numerous piglet uteri. Automated quantification of proliferating cell area, reducing analysis time from days to hours for biologists. Used image J for image analysis.

Language: MATLAB - Size: 3.42 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

DanuserLab/u-track3D

Multiple particle tracking in dense 3D particle fields complemented with dynamic regions of interest and trackability inferences for the automated exploration of large volumetric sequences.

Language: MATLAB - Size: 55.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 2

DanuserLab/u-inferforce

u-inferforce (Traction Force Microscopy) is a MATLAB software that reconstructs traction forces of cells adhered on elastic gel doped with beads.

Language: MATLAB - Size: 79.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 3

DanuserLab/Isogai-ARP23-Paper-2025

Language: Python - Size: 146 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

SilasBoyeNissen/song2023

"Protein phosphatase 1 regulates core PCP signaling" published in EMBO reports (2023)

Language: MATLAB - Size: 1.83 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

SilasBoyeNissen/TranscriptionalHeterogeneityAndCellCycleRegulationAsCentralDeterminantsOfPrimitiveEndodermPriming

"Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming" published in eLife (2022)

Language: MATLAB - Size: 294 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

DanuserLab/u-shape3D

Detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.

Language: MATLAB - Size: 107 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 29 - Forks: 6

DanuserLab/u-delineate

A Matlab package for segmentation of filament and the orientation.

Language: MATLAB - Size: 76.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

DanuserLab/u-segment

A Matlab software package to do 2D cell segmentation.

Language: MATLAB - Size: 76.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

cgeils25/White_Blood_Cell_Image_Classification

White blood cell image classification with fine-tuned ResNet-18

Language: Jupyter Notebook - Size: 41.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

Sentinal4D/cellshape

3D shape analysis using deep learning

Language: Python - Size: 5.5 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 6

pertzlab/ARCOS-tutorial

A Jupyter notebook to identify collective cell signalling in raw microscopy images

Language: Jupyter Notebook - Size: 7.87 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

fberkemeier/Notch-Delta-Coupling

Source code for "Coupling dynamics of 2D Notch-Delta signalling", by Francisco Berkemeier and Karen M. Page

Language: Mathematica - Size: 62.7 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

sarisabban/SinfNet

A collection of datasets and neural networks for microorganism image classification

Language: HTML - Size: 53.4 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 1

ieee8023/countception

Count-Ception: Counting by Fully Convolutional Redundant Counting

Language: Jupyter Notebook - Size: 118 MB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 51 - Forks: 14

oist/Usiigaci

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

Language: Jupyter Notebook - Size: 459 MB - Last synced at: 3 months ago - Pushed at: almost 5 years ago - Stars: 195 - Forks: 68

AllenCellModeling/pytorch_integrated_cell

Integrated Cell project implemented in pytorch

Language: Python - Size: 125 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 44 - Forks: 13

DanuserLab/Driscoll-Worrying-Paper

Python code used to detect and track blebs frame-to-frame, and to analyze bleb size statistics before and after photoactivation.

Language: Python - Size: 51.8 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

tlo-bot/omnisegger

OmniSegger - from the Wiggins Lab at UW

Language: MATLAB - Size: 74.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 9 - Forks: 4

KarrLab/wc_model_gen

Framework for systematically and scalably designing whole-cell models from large datasets

Language: Python - Size: 11.3 MB - Last synced at: 28 days ago - Pushed at: 6 months ago - Stars: 6 - Forks: 2

Shuyib/cell-explorer-tool

An image explorer tool that uses ipywidgets and image manipulation in Pillow to look for and refine features in a image. This is mostly pitched on cell biology, cytopathology and histopathology.

Language: Jupyter Notebook - Size: 734 KB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 1

SPARCED/SPARCED

Mechanistic Pan-Cancer Signaling Model

Language: Jupyter Notebook - Size: 76.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 4

deweylab/CellO

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

Language: Jupyter Notebook - Size: 21.9 MB - Last synced at: 28 days ago - Pushed at: about 2 years ago - Stars: 65 - Forks: 15

AllenCellModeling/actk

Automated Cell Toolkit

Language: Python - Size: 6.61 MB - Last synced at: 12 days ago - Pushed at: over 4 years ago - Stars: 24 - Forks: 4

IBT-FMI/ABI-connectivity-data_generator

Generate a package-manager-friendly archive of ABI connectivity maps registered in SAMRI standard space.

Language: Python - Size: 3.61 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

praneet1988/ELeFHAnt

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classifiers 1) RF 2) SVM and 3) LR

Language: R - Size: 61.2 MB - Last synced at: 8 months ago - Pushed at: about 3 years ago - Stars: 20 - Forks: 6

meyer-lab/tHMM

A general Python framework for using hidden Markov models on binary trees or cell lineage trees.

Language: Python - Size: 63.3 MB - Last synced at: 28 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 1

arnaublanco/Fluospotter

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

Language: Python - Size: 56.3 MB - Last synced at: 26 days ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

LSeu-Open/Cellpose_Gradio

A Gradio based user-friendly interface for cell segmentation using Cellpose

Language: Python - Size: 2.24 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

pskeshu/brushstrokes

A post-modern microscope software

Language: Python - Size: 4.88 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

phydev/SPiCCAto

Software developed to study the influence of the extracellular matrix in cell migration.

Language: Fortran - Size: 4.35 MB - Last synced at: 4 months ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 1

LuisCoy/CoyBioinformatics

Functions for proteomic analysis and more

Language: R - Size: 322 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

KarrLab/wc_rules

Rule-based modeling for whole-cell models.

Language: Python - Size: 1.41 MB - Last synced at: 28 days ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 3

Turku-BioImaging/ColonyArea

ImageJ-plugin that performs standard analysis of colony formation assays conducted in 6- to 24-well dishes.

Language: ImageJ Macro - Size: 13.1 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

junelsolis/fluorescent-nuclei-analysis

Demonstration on fluorescent nuclei segmentation using pre-trained AI

Language: Python - Size: 27.3 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Beth526/metis_project_4

NLP on biology paper abstracts

Language: Jupyter Notebook - Size: 61.5 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

geometric-intelligence/cellgeometry

A web-based application for Cell Shape Analysis.

Language: Jupyter Notebook - Size: 53.9 MB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

Jeff-Gui/PCNAdeep

Track single-cells and profile the cell cycle with PCNA images.

Language: Python - Size: 74.5 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

alexisjapas/napari-vesicles-segmentation 📦

A simple plugin to detect vesicles in cells images.

Language: Python - Size: 1.19 MB - Last synced at: 1 day ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0

CLO-ontology/CLO

Communitiy-based Cell Line Ontology

Language: Shell - Size: 77.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 4

shliamin/OpenCV-Mitosis-Detection

This repository contains a Python application using OpenCV for detecting mitosis in images. Aimed at researchers and biologists, it provides tools to automate the counting and identification of mitotic figures in microscopic images, supporting studies in cellular biology and medical diagnostics.

Language: Jupyter Notebook - Size: 85.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0