QuPath - Open-source bioimage analysis for research

Integrated Cell project implemented in pytorch

Shape-Out has been superseded by Shape-Out 2.

Track 2D cell motion and mitosis in time-lapse microscopy

manipulation and analysis of phase microscopy data

This remote module contains classes related to segmentation of biological cells. It has classes to represent cells' shape, color, and growth state. It also has classes to represent a cell genome, whose expression is modeled by differential equations.

A small tool in python to read the bright-field image data and the phase image data recovered from a Digital holographic microscope (DHM) and segment the nuclei to calculate physical parameters like roughness and volume.

High Intensity Peak Analysis for detecting High Intensity Cells

A web-based application for Cell Shape Analysis.

Visualize similar cells on a 2D plot using t-SNE

HIPA Tool GUI

GO Webapp for the HIPA Tool

A script to plot traces of muscle contractions from video recordings. This is part of my ongoing PhD work.

Convert experiment dataset of cells into one csv format.

Deep Learning based segmentation and tracking to understand the dynamics and morphology of cells over time.

Repository for publication outlining a number of computational models for complex wound analysis in both mice and humans.

Repository for publication outlining a number of computational models for complex wound analysis in both mice and humans.