2017 Winter Project Week/ImprovementsToSegmentEditor

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Home < 2017 Winter Project Week < ImprovementsToSegmentEditor

Key Investigators

  • Csaba Pinter (Queen's)
  • Andras Lasso (Queen's)

Project Description

Objective Approach and Plan Progress and Next Steps
  • Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images
  • The module is quite new, so we'd love to
    • help people adopt the new module
    • hear any feedback about the module
  • Breakout session in Kiva room at 12PM on Wednesday
  • About 30 participants. Presentation + demo + discussion
  • Basics of the underlying Segmentations infrastructure presented (Csaba): these slides (PDF) (This is a longer version of the slides presented. More information on the Segmentations module wiki page)
  • Segment Editor features presented (Andras)
    • CTACardio
      • Thresholding
        • Apply
        • Crop right arm with scissors in slice view, circle ROI
        • Create model
        • Undo
        • Use for paint
      • Paint:
        • Segment vessel in right arm
        • Create model
        • Change spacing
        • Sphere paint
      • Hollow model:
        • Copy segment
        • Grow segment
        • Subtract segment
        • Cut ends
      • Masking:
        • Editable area: inside all segments
        • Paint
        • Grow
        • New segment, Outside all segments
        • Grow
        • New segment, Overwrite other segments (default)
        • Paint
        • Overwrite other segments: None
    • Auto-complete:
      • Geometric:
        • CTACardio
        • Abdominal muscles
      • Growcut
        • MRBrainTumor1
        • Growcut
        • Fix leakage
        • Smoothing
        • Segment stats
    • Scissors:
      • CTChest, bone threshold
      • Island / Keep largest
      • Create surface
      • Create new segment (for ribs)
      • Editable: inside all
      • Scissors - fill outside
      • Split islands to segments
      • Separate lowest vertebra with 3d scissors
    • Slice thickness is used by paint tool 2D size
    • Segmentation on oblique slices
    • Segmentation on vesselness filtering result
  • Video coming soon
  • Discussion meeting minutes
    • Rename Apply for paint to Use as mask in all effects (in Threshold)
    • Logical/Copy -> Copy from
    • Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)
    • Clipping circle, adding margin (Adam)
    • First master volume resolution remains the segment resolution -> make it clearer?
      • Explain master volume in a tooltip or similar
    • Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)
    • Alexis' comments
      • Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)
      • Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)
      • Auto-complete contains very different operations -> make it two buttons?
    • Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)
    • Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?
    • 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking
    • Template effect extension
    • Volume clip features in segment editor (Christian) -> User interactions might be problematic

Background and References

Feedbacks and status of implementation

  • To be processed
    • Rename Apply for paint to Use as mask in all effects (in Threshold)
    • Logical/Copy -> Copy from
    • Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)
    • Clipping circle, adding margin (Adam)
    • First master volume resolution remains the segment resolution -> make it clearer?
      • Explain master volume in a tooltip or similar
    • Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)
    • Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)
    • Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)
    • Auto-complete contains very different operations -> make it two buttons?
    • Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)
    • Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?
    • 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking
    • Template effect extension
    • Volume clip features in segment editor (Christian) -> User interactions might be problematic
    • Lots of wasted space around effect buttons
    • Place large undo/redo buttons below effect list? -> would waste valuable vertical space
    • Work more with meaningful icons/buttons (including tooltips) which would improve the overall user experience. Specifically:
      • Shrink and grow could be replaced by checkable buttons that symbolize shrink/grow
    • Make effects work on grayscale images (maybe convert when we resample?)
    • Draw text (on 3D, maybe on 2D; could be implemented by creating the mask by a scissor-like method and then grow or erode the segment)
    • Mirror segment along axis (typically needed for using healthy side as a template for reconstructing damaged side)
    • Fixed-radius circle scissors (allow define and accurate diameter using a spinbox and draw it by a single click)
    • Add more keyboard shortcuts (not just for effect 1-6)
    • RGB images cannot be edited directly