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https://projectweek.na-mic.org
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Project: WSI-DICOM Improvement - From Viewer to Analysis #868

Closed FabianHoerst closed 10 months ago

FabianHoerst commented 10 months ago

Draft Status

Ready - team will start page creating immediately

Category

VR/AR and Rendering

Presenter Location

In-person

Key Investigators

Project Description

Despite various existing solutions for the conversion of WSI data into DICOM, there is a distinct lack of conversion tools (vendor agnostic) that result in DICOM files. Current solutions fall short in generating DICOM files compatible with OpenSlide (4.0.0) and OHIF/SLIM-Viewer, including a PACS, impeding seamless integration and compromising overall performance.

Our objective is to 1. assess available conversion tools, 2. examine their seamless integration capabilities, and 3. enhance or develop our own solutions for WSI-DICOM conversion that integrates into PACS systems connected to web-based viewers (OHIF/SLIM), but also works locally with open-source Viewers such like QuPath (newest version 0.5.0). As automatic slide analysis with AI algorithms (mostly Python) is a cornerstone of computational pathology, OpenSlide integration is another necessary requirement.

Objective

This project aims to test existing software solutions for vendor-agnostic WSI to DICOM conversion in digital pathology and deliver/develop an open-source, community-maintained software solution. The tool must adhere to established software design patterns, ensuring ease of contribution from the community.

Approach and Plan

  1. Provide a testing suite for testing resulting DICOM files, consisting of PACS/Viewer/Analysis-Components
  2. Test existing WSI DICOM solutions and find shortcomings
  3. Develop/Improve WSI DICOM conversions
  4. Deliver key insights into shortcomings to push conversion forward

Progress and Next Steps

Next steps are to build the test suite in advance, prepare test data and begin to collect more tools

Illustrations

idea

Background and References

Current known solutions for the WSI-DICOM Conversion:

thanks to @dclunie

  1. bfconvert (BioFormats): Converting a file to different format — Bio-Formats 7.1.0 documentation. Link: https://bioformats.readthedocs.io/en/v7.1.0/users/comlinetools/conversion.html
  2. dicom_wsi Gu Q, Prodduturi N, Jiang J, Flotte TJ, Hart SN. Dicom_wsi: A Python Implementation for Converting Whole-Slide Images to Digital Imaging and Communications in Medicine Compliant Files. J Pathol Inform. 2021;12(1):21. doi:10.4103/jpi.jpi_88_20 Link: https://github.com/Steven-N-Hart/dicom_wsi
  3. GoogleCloudPlatform. WSI to DICOM Converter. Google Cloud Platform; 2022. Link: https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter
  4. wsidicomizer. Sectra AB Sectra AB. wsidicomizer. imi-bigpicture; 2021. Link: https://github.com/imi-bigpicture/wsidicomizer
  5. Jodogne S, Lenaerts É, Marquet L, Erpicum C, Greimers R, Gillet P, et al. Open Implementation of DICOM for Whole-Slide Microscopic Imaging: In: Proceedings of the 12th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications. Porto, Portugal: SCITEPRESS - Science and Technology Publications; 2017. p. 81–7. Available from: https://orbi.uliege.be/handle/2268/204498 doi:10.5220/0006155100810087
  6. Clunie D. com.pixelmed.convert.TIFFToDicom. Link: http://www.dclunie.com/pixelmed/software/javadoc/com/pixelmed/convert/TIFFToDicom.html
  7. Pocock J. wsic. 2023. Link: https://github.com/John-P/wsic
  8. Orthanc WSI "Dicomizer" Link: https://www.orthanc-server.com/static.php?page=wsi Documentation: https://orthanc.uclouvain.be/book/plugins/wsi.html

Background Information

DICOM-WSI: https://dicom.nema.org/dicom/dicomwsi/

Test Data

OpenSlide: https://openslide.org/ Test data can be downloaded there for some vendors.

Other Resources

Test-Suite: TBD Link to Lean Study Host: https://github.com/TIO-IKIM/LeanStudyHost

github-actions[bot] commented 10 months ago

Project Page Pull Request Creation

:white_check_mark: COMPLETED: See https://github.com/NA-MIC/ProjectWeek/pull/883