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organoids

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quadbio /VoxHunt

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

single-cell organoids

UpdatedMar 1, 2024
HTML

OrgaQuant

TKassis /OrgaQuant

Organoid Localization and Quantification Using Deep Convolutional Neural Networks

biology stemcells keras-retinanet organoids

UpdatedJan 22, 2022
Python

mims-harvard /PROTON

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

drug-repurposing alzheimers-disease parkinsons-disease neurology organoids bipolar-disorder ai-for-science graph-ai

UpdatedDec 27, 2025
Jupyter Notebook

jn-goe /gruffi

Granular Functional Filtering (Gruffi) to isolate stressed cells

geneontology scrna-seq-analysis filtering-algorithm organoids

UpdatedNov 7, 2024
R

monarch-initiative /namo

standards artificial-intelligence ontologies monarchinitiative obofoundry organoids linkml new-approach-methodologies ai4curation model-systems

UpdatedDec 8, 2025
Python

lazappi /phd-thesis-analysis

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

rna-seq analysis kidney scrna-seq phd-thesis single-cell single-cell-rna-seq organoids analysis-website

UpdatedOct 15, 2019
R

TAPE-Lab /CyGNAL

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

visualization visualisation pca data-analysis ptm fcs umap mass emd cytof cytometry signalling cytobank ptms organoids cell-communication-lab scprep dremi tape-lab

UpdatedDec 7, 2023
Python

cancersysbio /gastric_organoid_evolution

Deterministic evolution and stringent selection during pre-neoplasia

genomics cancer-genomics tumor-evolution organoids gastric

UpdatedJun 3, 2023
HTML

mzabolocki /fusion_org_ephys

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

signal-processing calcium-imaging probes optogenetics extracellular-recordings organoids multi-unit

UpdatedDec 5, 2023
Jupyter Notebook

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

Human brain organoids connected to silicon computers

organoids brain-on-a-chip bio-hybrid-computing biological-computing dishbrain

UpdatedOct 31, 2023

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

bacteria bci brain-computer-interface neural-link organoids neural-interfaces human-brain-organoid

UpdatedOct 31, 2023

leandrenash /Learning-Capacity-Simulation-for-Organoids

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).

simulation simulation-environment organoids organoid-intelligence organoid-learning

UpdatedMar 12, 2025
Python

bardylab /miscos_org_ephys

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

signal-processing calcium-imaging probes optogenetics extracellular-recordings optogenetics-stimulation organoids multi-unit

UpdatedDec 5, 2023
Jupyter Notebook

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 athttps://www.biorxiv.org/content/10.1101/2024.02.12.580032v1. Demo application available athttps://segmentorganoids.streamlit.app/

deep-learning organoids cellpose stardist organoid-segmentation

UpdatedJul 5, 2024
Jupyter Notebook

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.

imagej quantification thresholding opencv2 colocalization organoids

UpdatedJun 29, 2024
Python

LittleQBerry /TransOrga

Oraganoid segmentation tool

segmentation organoids

UpdatedJul 18, 2023
Python

Edgar-Galan /organoid-profiler

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

segmentation organoids morphology-metrics

UpdatedJan 29, 2026
Jupyter Notebook

rafa-lab-git /Teaching-Material-and-Lectures

Lectures slides for BSc and MSc students

cancer disease metabolism metabolomics organoids

UpdatedJan 28, 2025

Shaun-Regenbaum /hu-glioblastoma

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

bioinformatics biology glioblastoma organoids glioblastoma-drug-discovery

UpdatedDec 28, 2025
Jupyter Notebook

alex-merge /Organoid-Analyzing-Tools

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

UpdatedSep 21, 2022
Python

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