maples-dr 0.1.0rc3

Utilities python library for the public dataset: MAPLES-DR.

MAPLES-DR

MAPLES-DR (MESSIDOR Anatomical and Pathological Labels for Explainable Screening of Diabetic Retinopathy) is a public dataset which provides diagnoses for DR and ME as well as pixel-wise segmentation maps for 10 retinal structures for 198 images of MESSIDOR. This repository provides a python library of utility codes to ease the use of the database.

MAPLES-DR Dataset Content

MAPLES-DR dataset is available for download on figshare. The fundus images are not included in MAPLES-DR but one can download them from MESSIDOR Consortium's website.

If you use the MAPLES-DR dataset, please cite the following paper: https://arxiv.org/abs/2402.04258.

MAPLES-DR Python Library

The maples_dr python library provides a simple way to download and use the dataset. It was designed with machine learning applications in mind.

Install

pip install maples-dr

If you plan to run the examples provided as Jupyter Notebooks in the examples/ folder, you should also install their dependencies:

pip install maples-dr[examples]

Simple Usage

Load MAPLES-DR in memory

Once imported, MAPLES-DR train or test sets can be loaded in memory with a single line of Python code.

import maples_dr
train_set = maples_dr.load_train_set()
test_set = maples_dr.load_test_set()

If necessary, the dataset archive is automatically downloaded from Figshare, extracted and cached locally. The data is then returned as a Dataset object assimilable to a list of samples stored as dictionnaries containing all MAPLES-DR labels.

For example, the vessel map of the first sample of the train set can be accessed with:

    vessel_map = train_set[0]['vessels']

Export MAPLES-DR to a local folder

Alternatively, MAPLES-DR images can be saved in local folders:

    maples_dr.export_train_set('MAPLES-DR/train/')
    maples_dr.export_test_set('MAPLES-DR/test/')

For more information on how to configure image resolution and format, how to include the fundus images along the labels, and more advanced functionalities, have a look at the documentation of maples_dr!

Examples

The examples/ folder contains Jupyter Notebooks that demonstrate how to use the maples_dr python library.

• article_figures.ipynb generates all the figures of MAPLES-DR paper.
• display_biomarkers.ipynb uses maples-dr to download and visualize the anatomical and pathological structures of the retina on top of the fundus images from MAPLES-DR.