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Slicer Case Iterator
- Joost van Griethuysen (The Netherlands Cancer Institute)
- Steve Pieper (Isomics)
This project aims to expand the usage of Slicer Case Iterator to work with DICOM(WEB) backend to support workflows where the data is available in DICOM format.
- Generalize internal batch definition to allow different input modes (CSV, DICOM)
- Link to Slicers DICOM browser to retrieve images
- Implement prefetching of next n cases to speed up processing
- Store segmentation results as DICOM SEG objects
Approach and Plan
- Create class implementing generator to hold batch, with different input methods a inherited subclasses
- Talk to Slicer developers on how to best approach this (what kind of identifiers, methods to use, etc.)
- Closely related to point above. Investigate on how to analyze input to determine best conversion step, how to store results of this evaluation.
- Talk to Slicer developers on how to store a Slicer Segmentation object as DICOM SEG object (when input image is DICOM format)
Progress and Next Steps
- Done, merged with master in PR #7
- Using SeriesUID, it is now possible to load series using the Slicers DICOM database. Not yet merged with the master PR #8
- In DICOM input, series is first checked for loadables using MultiVolumeImporterPlugin and if necessary, by DICOMScalarVolumePlugin. Not yet possible to do this using a type of prefetch, or parallel processing.
- Add possibility to store Segmentations as DICOM SEG objects
- Add example scripts to help users generate the input tables for their datasets
- Investigate use of DICOM Web UPS / Modality Work List to define the batch
Background and References