https://github.com/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/
https://github.com/ajinkya-kulkarni/pyorganoidnet

cellpose deep-learning organoid-segmentation organoids stardist

Last synced: 5 days ago
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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/

• Host: GitHub
• URL: https://github.com/ajinkya-kulkarni/pyorganoidnet
• Owner: ajinkya-kulkarni
• License: gpl-3.0
• Created: 2023-09-09T08:54:49.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-07-05T07:38:56.000Z (almost 2 years ago)
• Last Synced: 2025-09-04T19:50:01.718Z (9 months ago)
• Topics: cellpose, deep-learning, organoid-segmentation, organoids, stardist
• Language: Jupyter Notebook
• Homepage: https://zenodo.org/records/10643410
• Size: 60.9 MB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

          
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# OrganoIDNetData: Pancreatic Ductal Adenocarcinoma Organoid Dataset

## Introduction

Welcome to the OrganoIDNetData repository. This public dataset is a significant step forward in cancer research, particularly in the study of Pancreatic Ductal Adenocarcinoma (PDAC). It comprises phase-contrast images of murine and patient-derived tumor organoids co-cultured with immune cells. With 190 images and 33,906 organoids, OrganoIDNetData serves as a potential benchmark for organoid segmentation models in oncological research.

The pre-print based on this work can be found [here](https://www.biorxiv.org/content/10.1101/2024.02.12.580032v1.full.pdf).

## Dataset Overview

- **Type of Cancer:** Pancreatic Ductal Adenocarcinoma

- **Images:** 190 phase-contrast images

- **Organoids Count:** 33,906

- **Culturing:** Co-cultured with immune cells

- **Focus:** Tumor organoids

## Objective

The primary objective of OrganoIDNetData is to address the challenges in organoid research, particularly:

- Efficient and reliable segmentation of organoid images

- Quantification of organoid growth, regression, and response to treatments

- Prediction of organoid system behaviors

## Usage

This dataset is intended for use in developing and testing algorithms for:

- Object detection and segmentation in organoid images

- Machine learning models in oncology research

- Benchmarking against other organoid segmentation models

## Contributing

We welcome contributions to OrganoIDNetData! If you have suggestions or improvements, please fork the repository and submit a pull request.