VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

Organoid Localization and Quantification Using Deep Convolutional Neural Networks

Granular Functional Filtering (Gruffi) to isolate stressed cells

Pipeline for analysing and visualising CyTOF datasets, with a focus on PTM signalling networks.

Code for the analysis chapter of my PhD thesis looking at kidney organoid scRNA-seq data

Deterministic evolution and stringent selection during pre-neoplasia

Multi-unit spike analysis in ventral midbrain-striatal-cortical organoids (MISCOs) pre- and post- optogenetic stimulation.

Human brain organoids connected to silicon computers

Bacterial colonies attaching themselves to human brain organoids, as a neural link to a silicon computer

This repository provides StarDist and CellPose models, meticulously trained on a large dataset of Pancreatic Ductal Adenocarcinoma organoids co-cultured with immune cells. Pre-print available at https://www.biorxiv.org/content/10.1101/2024.02.12.580032v1. Demo application available at https://segmentorganoids.streamlit.app/

Preprocess, noise-reduction, threshold & quantify images to get box plots for each class (mainly cell cultures of different cel llines). Colocalization due to a naive trick of counting all overlapping signals/pixels. Could be done in ImageJ as well, but i thought this is better suited than fiddling with macros.

A sophisticated scientific simulation platform for analyzing organoid learning capacity through cutting-edge machine learning and interactive data visualization. This platform enables researchers to simulate and analyze how organoids learn and adapt in response to various stimuli, focusing on Organoid Intelligence (OI) and Organoid Learning (OL).

Oraganoid segmentation tool

Electrophysiology analysis in ventral midbrain-striatal-cortical organoids (MISCOs) pre- and post- optogenetic stimulation.

Nuclear segmentation and quantification of organoid slices

Lectures slides for BSc and MSc students

Digtal Organoid On Chips

Robotic Generation and Kinetic Screening of Patient-Derived Glioblastoma Organoids Reveal Pharmaceutical Dynamics

Patient-derived organoids as predictive models for drug testing and repurposing in glioblastoma therapy

Organoid Analyzing Tools (OAT) is a package that allow you to analyze organoids dynamics.