DanuserLab/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

Language: MATLAB - Size: 79.2 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 50 - Forks: 21

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: 78.5 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 21 - Forks: 6

DanuserLab/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

Language: Python - Size: 5.52 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 8 - Forks: 1

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: 86.3 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 1 - 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: 18 days ago - Pushed at: 18 days ago - Stars: 28 - Forks: 3

DanuserLab/u-segment

A Matlab software package to do 2D cell segmentation.

Language: MATLAB - Size: 76.1 MB - Last synced at: 20 days ago - Pushed at: 20 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: 20 days ago - Pushed at: 20 days ago - Stars: 5 - Forks: 1

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: 20 days ago - Pushed at: 20 days ago - Stars: 7 - Forks: 1

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: 16 days ago - Pushed at: 3 months ago - Stars: 29 - Forks: 2

DanuserLab/biophysicsModels

This is a project of a membrane model

Language: MATLAB - Size: 2.05 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

DanuserLab/cmeAnalysis

clathrin-mediated endocytosis analysis

Language: MATLAB - Size: 81.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 1

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: about 2 months ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 1

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: 4 months ago - Pushed at: 4 months ago - Stars: 8 - Forks: 3

DanuserLab/Isogai-ARP23-Paper-2025

Language: Python - Size: 146 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - 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: 5 months ago - Pushed at: 5 months ago - Stars: 29 - Forks: 6

DanuserLab/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.

Language: MATLAB - Size: 100 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 10 - Forks: 2

DanuserLab/u-delineate

A Matlab package for segmentation of filament and the orientation.

Language: MATLAB - Size: 76.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

DanuserLab/nanes_2024_dev-cell_krt-signaling

Language: MATLAB - Size: 78 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

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: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

DanuserLab/openLCH Fork of andrewjUTSW/openLCH

Live Cell Histology: Extracting latent features from label-free live cell images using Adversarial Autoencoders

Language: Lua - Size: 13.6 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

DanuserLab/QFSM

Quantitative Fluorescent Speckle Microscopy

Language: MATLAB - Size: 67.4 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

DanuserLab/DeBias

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

Language: MATLAB - Size: 532 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 2

DanuserLab/GrowthConeAnalyzer Fork of mbagonis/GrowthConeAnalyzer

Language: MATLAB - Size: 199 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

DanuserLab/MonolayerKymographs Fork of assafzar/MonolayerKymographs

Monolayer spatiotemporal dynamics analysis.

Language: MATLAB - Size: 257 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

DanuserLab/Mask-Regularized-Diffeomorphic-Cell-Registration

Language: MATLAB - Size: 27.3 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

DanuserLab/Weems-Septin-Paper

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

Language: Python - Size: 74.1 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

DanuserLab/Protrusion_Retraction_Database

Language: R - Size: 4.91 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

DanuserLab/3dCellShape

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

Language: MATLAB - Size: 341 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0

DanuserLab/MorphodynamicProfiling Fork of xmameisu/MorphodynamicProfiling

Language: Matlab - Size: 1.06 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0