diff --git a/README.md b/README.md index 1241268..d5066a8 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,7 @@ app_file: demo/app.py [![license](https://img.shields.io/github/license/DAVFoundation/captain-n3m0.svg?style=flat-square)](https://github.com/DAVFoundation/captain-n3m0/blob/master/LICENSE) [![CI/CD](https://github.com/raidionics/AeroPath/actions/workflows/deploy.yml/badge.svg)](https://github.com/raidionics/AeroPath/actions/workflows/deploy.yml) +Open In Colab [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10069288.svg)](https://doi.org/10.5281/zenodo.10069288) [![paper](https://img.shields.io/badge/arXiv-preprint-D12424)](https://arxiv.org/abs/2311.01138) @@ -30,9 +31,29 @@ This repository contains the AeroPath dataset described in ["_AeroPath: An airwa The dataset is made openly available at [Zenodo](https://zenodo.org/records/10069289) and [the Hugging Face Hub](https://huggingface.co/datasets/andreped/AeroPath). Click any of the two hyperlinks to access the dataset. -## [Dataset structure](https://github.com/raidionics/AeroPath#data-structure) +## [Dataset](https://github.com/raidionics/AeroPath#data) -The dataset contains 27 CTs with corresponding airways and lung annotations. The folder structure is described below: +### [Accessing dataset](https://github.com/raidionics/AeroPath#accessing-dataset) + +The dataset contains 27 CTs with corresponding airways and lung annotations. The folder structure is described below. + +The easiest way to access the data is through Python with Hugging Face's [datasets](https://pypi.org/project/datasets/) package: +``` +from datasets import load_dataset + +# downloads data from Zenodo through the Hugging Face hub +# - might take several minutes (~5 minutes in CoLab) +dataset = load_dataset("andreped/AeroPath") +print(dataset) + +# list paths of all available patients and corresponding features (ct/airways/lungs) +for d in dataset["test"]: + print(d) +``` + +A detailed interactive demo on how to load and work with the data can be seen on CoLab: Open In Colab + +### [Dataset structure](https://github.com/raidionics/AeroPath#data-structure) ``` └── AeroPath.zip