Aachen Project

This repository contains source files of machine learning tools for medical tumor classification.

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Qupath Workflow

1. Download Qupath from https://github.com/qupath/qupath/releases/tag/v0.2.3 and unzip
2. Run Qupath by calling the binary file
3. Create Folder: mkdir project_aachen
4. in qupath file>create project and choose project_aachen
5. in qupath file>add image choose the tif (filename for example: 16-08510.tif)
6. now qupath is exporting some data in project_aachen there you find a folder named "data"
7. copy the annotations from the source folder into the data folder to see the annotations in qupath

Python

Make sure your python version matches the requirements listed in ''requirements.txt''! To make your life easy, I included ''conda-env.yml'' to match all python requirements with the help of conda. Simply create a new conda environment:

conda env create -f conda-env.yml 

and activate it:

conda activate conda-env

After all requirements match you may be able to execute our source code. All source files of the packages are included in the directory

./ml4medical/

You can execute the individual routines via in the folder via

import ml4medical 
ml4medical.myroutine()

or

form ml4medical import myroutine