https://github.com/imagingdatacommons/conversion_mirax_dicom
Code for the conversion of BMDeep dataset in MRXS format to DICOM format
https://github.com/imagingdatacommons/conversion_mirax_dicom
Last synced: 8 months ago
JSON representation
Code for the conversion of BMDeep dataset in MRXS format to DICOM format
- Host: GitHub
- URL: https://github.com/imagingdatacommons/conversion_mirax_dicom
- Owner: ImagingDataCommons
- License: bsd-3-clause
- Created: 2024-12-20T13:31:30.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-06-02T15:11:25.000Z (8 months ago)
- Last Synced: 2025-06-03T02:43:20.686Z (8 months ago)
- Language: Python
- Size: 300 KB
- Stars: 0
- Watchers: 8
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](https://doi.org/10.5281/zenodo.14933088) (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
2. bzcat