2017 Winter Project Week/ImprovementsToSegmentEditor

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  Projects List

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  Highlights of segmentations 1

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  Highlights of segmentations 2

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  Segmentation object

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

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)