QuPath - Open-source bioimage analysis for research

PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

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Shape-Out has been superseded by Shape-Out 2.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

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.

Implementation of HIDE as proposed in Völkl et al (2025), HIDE: Hierarchical cell-type Deconvolution

manipulation and analysis of phase microscopy data

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.

A web-based application for Cell Shape Analysis.

High Intensity Peak Analysis for detecting High Intensity Cells

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

ImageJ macro for neurite analysis in high content

A Repo for Nusa's Project from REGE-VUB

PhenoPixel: A web application for single-cell microscopy image analysis (deployed at Hiroshima University).

PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

PhenoPixel: A web application for single-cell microscopy image analysis (deployed at Hiroshima University).

PhenoPixel: A web application for single-cell microscopy image analysis (deployed at Hiroshima University).

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