2024.10.15 Weekly Meeting

[Sam_Horvath (Sam Horvath (Kitware))]

Today, we will be having our next weekly hangout at 10:00 AM ET until 11:00 AM ET

Anyone is welcome to join at this link: https://bit.ly/slicer-googlemeet-hosted-by-kitware

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Agenda:

Please post to this thread to put a topic on the agenda! We will try to prioritize agenda items during the meeting.

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Thanks
Sam and J-Christophe

[pieper (Steve Pieper (Isomics, Inc.))]

Let’s talk about plans for the 5.8 release.

[cpinter (Csaba Pinter)]

I hope there will be time to discuss Terminologies improvements, @muratmaga is joining as well. It would be great to agree on how to add creating custom terminology (see here).

[jcfr (Jean Christophe Fillion Robin (Kitware))]

Meeting Notes

Terminologies

• Module Improvements: Discussed potential enhancements to the Terminologies module. See the discussion here: Slicer Issue #6975.

• Terminology, Color Table, and Segment Relationship:

  • There is a significant disparity between the vast number of available terminology terms and the limited number of segments. The color table serves as a bridge:
    • Analogy: Terminology represents all available paint colors, the color table is the palette, and segments are the canvas.

• Handling Missing Terms:

  • It is not problematic if a segment lacks a corresponding term in the terminology. A streamlined editing approach could involve direct color table modifications. This would require an improved file format for color tables (details below).
  • Idea: Develop a new Terminologies extension to connect with an online repository of terminologies (e.g., on GitHub).

• Color Table File Format Enhancements:

  • Transition to CSV format, ensuring compatibility with scene load and save operations.
  • Include all essential terminology information: name, code, coding scheme designator, category, modifier, and optional anatomical location.
  • Allow for JSON properties to be optional, omitting unused entries.

• Displaying Color Tables in Terminology Contexts:

  • Limit to discrete options and filter based on specific attributes (e.g., “compatible”: adequate metadata).

• Creating a “Short List” Color Table:

  • Enable users to generate a new color table based on current segments, providing a customizable starting point.

• MorphoDepo (MorphoCloud) Requirements:

  • Each user receives a unique color table tied to their segmentation.
  • Consider features and ideas from the SegmentationVerification extension.

• Using Uberon in Terminologies:

  • Hierarchical structure required, such as categories (e.g., “skeletal system / spine”) to create a more organized tree structure, replacing the current flat list.

• Next Steps:

  • Enhance color tables to store metadata effectively.
  • Integrate color tables within the terminology selector for streamlined user experience.

Slicer & Trame

• Trame Integration:

  • Discussed the integration of trame with Slicer to support backend GPU rendering.

  • Render window content is converted into a compressed JPEG image, which is transmitted to the front end as a web application.

  • Transitioning to in-render window widgets would minimize dependencies on Qt.

  • Refactoring will be required to enable segmentation editor effects to function independently from Qt.

  • Progress related to Slicer refactoring is ongoing; see Commits · AlexyPellegrini/Slicer · GitHub

  • On-going development of trame-based Slicer should be released open-source in the first quarter of 2025. For questions, reach out to @finetjul, @Thibault_Pelletier and @jcfr

    

Telemetry

• Submitted Pull Requests:
  • A pull request has been submitted for the SlicerTelemetry repository.
  • Another pull request was submitted for the slicer-usage-stats repository.
  • Both PRs are under review.

Slicer 5.8 Release

• The release status of version 5.8 will be discussed in the upcoming meeting on October 22nd.