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wsidicomizer-based conversion into DICOM WSI format for Imaging Data Commons

Key Investigators

• Andrey Fedorov (BWH, USA)
• David Clunie (PixelMed Publishing, USA)
• Daniela Schacherer (Fraunhofer MEVIS, Germany)

Project Description

This project is motivated by the operational needs of the Imaging Data Commons to have a sustainable mechanisms supported by open-source software for harmonizing various slide microscopy images in vendor-specific representations into DICOM Whole Slide Imaging format. Our current procedures is not sustainable, since they rely on the PixelMed tools by David Clunie, which are based on a coding style and build process that has not changed since initiated over 20 years ago, unfortunately have “bus factor” of 1, and are not open for community contributions. We started using wsidicomizer as a replacement, but there are gaps in the functionality to be remedied, and additional testing that needs to be done before we can consider operational switch.

This project is the continuation of the earlier project at PW42 2025.

Objective

1. Implement routing of the DICOM metadata.
2. Evaluate extensibility of the conversion approach to various input types.

Approach and Plan

1. Improve the conversion script developed for the HMS SARDANA sample to handle metadata.
2. Evaluate conversion of the .czi samples.
3. Evaluate metadata routing in the Mirax conversion script

Progress and Next Steps

1. Describe specific steps you have actually done.

Illustrations

No response

Background and References

No response