cell-analysis

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

FLIM-focused framework for multimodal single-cell imaging: extract features from FLIM and QPI data, then analyze any tabular dataset interactively.

Shape-Out has been superseded by Shape-Out 2.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

manipulation and analysis of phase microscopy data

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

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

GO Webapp for the HIPA Tool

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

Data-management/glue layer for a cell-painting feature-extraction pipeline

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