organoids

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

Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems

Organoid Localization and Quantification Using Deep Convolutional Neural Networks

Granular Functional Filtering (Gruffi) to isolate stressed cells

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

Deterministic evolution and stringent selection during pre-neoplasia

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

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

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).

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

Automated, high-throughput, quantitative characterization of morphological features and fluorescence signals of organoid and spheroid cultures

This repository provides deep learning models trained on a large dataset of Pancreatic Ductal Adenocarcinoma Organoids co-cultured with immune cells.

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.

Multi-scale bioinformatics pipeline for patient-specific drug screening via computational simulation of patient-derived organoids. Integrates U-Net segmentation, agent-based cell simulation, QSAR drug modelling and PDE diffusion.

Open operating-system specification for biological neural networks — cortical organoids, MEA-coupled cultures, and their in-silico emulators. v0.1 draft with working L0 reference emulator (Izhikevich + Hodgkin-Huxley + STDP + migration).

Oraganoid segmentation tool

Headless Rust toolkit for MED64 electrophysiology recordings