single cell foundation model for Gene network inference and more

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

3D vertex model allowing scutoids

Mechanistic Pan-Cancer Signaling Model

A Matlab package for segmentation of filament and the orientation.

A Matlab software package to do 2D cell segmentation.

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.

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

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.

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

A Python package for analyzing XYZ positional data of moving objects over time

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 events resulting from occlusion or genuine aggregation and dissociation events

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

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

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.

Interactive deep learning whole-cell segmentation and thresholding using partial annotations

Generate a package-manager-friendly archive of ABI connectivity maps registered in SAMRI standard space.

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities