organoids

TKassis/OrgaQuant

Organoid Localization and Quantification Using Deep Convolutional Neural Networks

jn-goe/gruffi

Granular Functional Filtering (Gruffi) to isolate stressed cells

TAPE-Lab/CyGNAL

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

lazappi/phd-thesis-analysis

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

cancersysbio/gastric_organoid_evolution

Deterministic evolution and stringent selection during pre-neoplasia

mzabolocki/fusion_org_ephys

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

Unlimited-Research-Cooperative/Biological-Silicon-Hybrid-Computing

Human brain organoids connected to silicon computers

Unlimited-Research-Cooperative/Human-Brain-Organoid-Bacterial-Neural-Link

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

ajinkya-kulkarni/PyOrganoIDNet

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/

Scaramir/HD_colocalization

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.

bardylab/miscos_org_ephys

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

LittleQBerry/TransOrga

Oraganoid segmentation tool

alex-merge/Organoid-Analyzing-Tools

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

boutroslab/Supp_Funk_2021

jarnokoetsier/Exosomal-MicroRNA-Profile

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

js-ish/DOoC

Digtal Organoid On Chips

nobias-fht/harschnitz-organoid-nuclei

Nuclear segmentation and quantification of organoid slices

Shaun-Regenbaum/hu-glioblastoma

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