2024.10.15 Weekly Meeting

Community Weekly meetings
1

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

Agenda:

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

Thanks
Sam and J-Christophe

2

Let’s talk about plans for the 5.8 release.

3

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).

4

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:

  • 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

      image
      image1920×1020 143 KB

Telemetry

Slicer 5.8 Release

  • The release status of version 5.8 will be discussed in the upcoming meeting on October 22nd.
1 Like
5

Very nice looking app! Markups are in there, looks very promising.

Integrating Slicer with Trame would allow to create custom looking web app that is designed for the tasks without any excessive functionality.

Thank you for the information and efforts, look forward to progress on this!