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u-track
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 eventsu-shape3D
Detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.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.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.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.cmeAnalysis
clathrin-mediated endocytosis analysisu-inferforce
u-inferforce (Traction Force Microscopy) is a MATLAB software that reconstructs traction forces of cells adhered on elastic gel doped with beads.u-signal3D
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 signaling across morphologically diverse cell populations.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.u-register
Analyze local cell edge motions (e.g. protrusion and retraction) and to locally sample intracellular fluorescence signals in 2D fluorescence microscopy data.u-integrate
Pipeline for inference of Granger-causal relations in molecular systems to study actin regulation in lamellipodia3dCellShape
3dCellShape implements measurement and analysis of geometric features on extracted 3D volumes of single cells from fluorescent imaging data.DeBias
DeBias decouples global bias from direct interactions in co-orientation and co-localization data.Protrusion_Retraction_Database
The usage of the protrusion/retraction packageu-segment
A Matlab software package to do 2D cell segmentation.Driscoll-Worrying-Paper
Python code used to detect and track blebs frame-to-frame, and to analyze bleb size statistics before and after photoactivation.Weems-Septin-Paper
Several post-processing scripts that analyze signal distributions on and near uShape3D-generated cell surfaces.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.Love Open Source and this site? Check out how you can help us