README.md

BoneMarrowWSI-PediatricLeukemia dataset conversion

--- This repository is still work in progress ---

This repository contains the code that was used for the conversion of the BoneMarrowWSI-PediatricLeukemia (aka BMDeep) dataset into DICOM format for ingestion into IDC.

This repository includes:

1. code for image conversion from MRXS to DICOM.
2. code for annotation conversion from CSV to DICOM.

Both are implemented to be run on a local machine, while retrieving actual data and returning converted results from/to a mounted server called Gaia.

Requirements

• see requirements.txt
• for running the verification scripts: installation of dicom3tools required
  1. wget https://dclunie.com/dicom3tools/workinprogress/dicom3tools_1.00.snapshot.20250128115421.tar.bz2 (or the most recent version available at https://dclunie.com/dicom3tools/workinprogress/index.html)
  2. bzcat <dicom3tools_1.00.snapshot.20250128115421.tar.bz2 | tar -xf
  3. mv dicom3tools_1.00.snapshot.20250128115421 dicom3tools
  4. sudo apt-get install xutils-dev
  5. cd dicom3tools && ./Configure && imake -I./config -DInstallInTopDir && make World && make install

Documentation