Complete analysis code for Bland et al., 2023

A Matlab software package to do 2D cell segmentation.

A Matlab package for segmentation of filament and the orientation.

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

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

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

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

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.

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

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.

Functions for proteomic analysis and more

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.

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

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

A curated list of repositories featuring articles, software, tools, pipelines, plugins, and more for biology research needs.

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.

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

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

clathrin-mediated endocytosis analysis

A multicellular physics simulation in Unreal Engine.