Digtal Organoid On Chips

Nuclear segmentation and quantification of organoid slices

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

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

Involvement of Extracellular Vesicle-derived miRNA clusters in Developing Healthy and Rett Syndrome Brain Organoids

Oraganoid segmentation tool

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

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.

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

Human brain organoids connected to silicon computers

Deterministic evolution and stringent selection during pre-neoplasia

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

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

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

Granular Functional Filtering (Gruffi) to isolate stressed cells

Organoid Localization and Quantification Using Deep Convolutional Neural Networks

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