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Conversion of bone marrow smear dataset from MIRAX format into DICOM

Key Investigators

Project Description

As the DICOM standard is increasingly used in digital pathology imaging, conversion of available datasets from proprietary formats into DICOM format can make the data more FAIR and improve transparency and reproducibility of research conducted with these data. For this reason, the NCI Imaging Data Commons (IDC) hosts all its data in DICOM format.

A set of bone marrow smear WSI available in MIRAX (.mrxs) format are to be ingested into the IDC. For that purpose they need to be converted into DICOM (.dcm) along with all available image and clinical metadata. In addition, this dataset contains extensive deep-learning generated nuclei annotations (bounding boxes) that should also be converted in DICOM in a suitable way.

Objective

  1. Objective A: Have a working script for the conversion of the complete set of bone marrow smear WSI into DICOM format based on wsidicomizer.
  2. Objective B: Include clinical metadata in an IDC-conformant way.
  3. Objective C (optional): Have a script that converts the nuclei annotations into DICOM.

Approach and Plan

Objective A

  1. Implement and verify code for conversion of the .mrxs files as is into .dcm. See also this issue: https://github.com/imi-bigpicture/wsidicomizer/issues/56
  2. Add code for ingestion of metadata that are not obtained from the .mrxs files / correct potential falsely estimated metadata.
  3. Have a few successfully converted samples and be ready to run code on complete collection.

Objective B

  1. Prepare additional clinical and lab data as table such that they can be ingested into IDC as BigQuery table.

Progress and Next Steps

  1. Describe specific steps you have actually done.

Illustrations

No response

Background and References

Background reading:

Further resources: