Danuser Lab's repositories
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 events
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.
cmeAnalysis
clathrin-mediated endocytosis analysis
u-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-infotrace
Compute causal relationships between individual pixels in 2D videos over space and time to reveal salient dynamics using a variety of causal measures
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 lamellipodia
3dCellShape
3dCellShape implements measurement and analysis of geometric features on extracted 3D volumes of single cells from fluorescent imaging data.
Driscoll-Worrying-Paper
Python code used to detect and track blebs frame-to-frame, and to analyze bleb size statistics before and after photoactivation.
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.
Protrusion_Retraction_Database
The usage of the protrusion/retraction package
Weems-Septin-Paper
Several post-processing scripts that analyze signal distributions on and near uShape3D-generated cell surfaces.
biophysicsModels
This is a project of a membrane model
GrowthConeAnalyzer
Growth Cone Analyzer pipeline
Mask-Regularized-Diffeomorphic-Cell-Registration
Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes
MonolayerKymographs
Monolayer spatiotemporal dynamics analysis.
MorphodynamicProfiling
Profiling cellular morphodynamics by spatiotemporal spectrum decomposition.
QFSM
Quantitative Fluorescent Speckle Microscopy
u-delineate
A Matlab package for segmentation of filament and the orientation.