Project-MONAI / Project-MONAI/MONAILabel

Secondary Capture Images and Send to XNAT

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Dominant language
Python
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Forks
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15h 41m
Merged PRs (30d)
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Description

Is your feature request related to a problem? Please describe.
Segmentation viewing and export to PACS/VNAs outside of the integrated OHIF viewer and/or Slicer. In order to integrate inference predictions/segmentations into routine clinical use, it is important that our segmentations be visible to clinicians. Images must be saved as dicom, inheriting all UID SOPs and other tags from the original acquisition.

Describe the solution you'd like
Could we implement Secondary Capture images into the main branch? Specifically I am interested in displaying segmentations as an overlay on top of the original images (with an alpha of approximately 0.5). This will require conversion of the photometric interpretation tag (0028,0004) from monochrome 2 to RGB, introducing intensity scaling issues of course.

Additional features:

  1. calculation of segmentation volumes
  2. additional SC images with segmentation volumes burned on to images (reports)

Describe alternatives you've considered

  1. The dicom SEG solution is one alternative that you have already implemented (thank you Ahmed!), but unfortunately not all PACS viewers are capable of loading dicom SEG files. While the solution works perfectly in the OHIF viewer, this limits integration into clinical operations including other PACS/VNAs.

  2. I have also considered SC image generation on the XNAT server side (which could be run as a container), but it may be more efficient to do this on the MonaiLabel server, where the numpy array has been returned by the inference prediction.

Additional context
Add any other context or screenshots about the feature request here.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the existing DICOM SEG implementation and the MONAI Label server path where the inference prediction returns a numpy array; compare this with the proposed XNAT-side container approach. Done requires an agreed scope for overlay Secondary Capture output, inherited DICOM metadata, volume calculation, and burned-in reports, with validation identified.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
computer-vision
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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