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.

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

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

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.

OmniSegger - from the Wiggins Lab at UW

clathrin-mediated endocytosis analysis

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

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.

Easy-to-use traction force microscopy (TFM) software

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

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

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

MATLAB codes developed in Courtemanche lab at University of Minnesota for automating analysis of actin filament properties from single molecule microscopy images.

A Matlab software package to do 2D cell segmentation.

A Matlab package for segmentation of filament and the orientation.

PIV-based tools for measuring collective cell migration

"Cluster Assembly Dynamics Drive Fidelity of Planar Cell Polarity Polarization" published in bioRxiv (2025)

"Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming" published in eLife (2022)

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.