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

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.

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.

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.

clathrin-mediated endocytosis analysis

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 even…

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.

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

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

Compute causal relationships between individual pixels in 2D videos over space and time to reveal salient dynamics using a variety of causal measures

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

A Matlab package for segmentation of filament and the orientation.

A Matlab software package to do 2D cell segmentation.

This is a project of a membrane model

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

The computational platform u-signal3D defines a shape-invariant representation of the spatial scales of molecular organization at the cell surface, enabling comparison and machine-learning of signa…

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

The usage of the protrusion/retraction package

3dCellShape implements measurement and analysis of geometric features on extracted 3D volumes of single cells from fluorescent imaging data.

Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes

Several post-processing scripts that analyze signal distributions on and near uShape3D-generated cell surfaces.

DeBias decouples global bias from direct interactions in co-orientation and co-localization data.

Quantitative Fluorescent Speckle Microscopy