Difference between revisions of "2017 Winter Project Week/ImprovementsToSegmentEditor"

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<gallery>
 
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Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
 +
Image:SegmentationHighlights01s.png|Highlights of segmentations 1
 +
Image:SegmentationHighlights02s.png|Highlights of segmentations 2
 +
Image:20160526_SegmentationObject.PNG|Segmentation object
 
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" -->
 
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</gallery>
 
</gallery>
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==Key Investigators==
 
==Key Investigators==
 
* Csaba Pinter (Queen's)
 
* Csaba Pinter (Queen's)
−
* Andras (Queen's)
+
* Andras Lasso (Queen's)
  
 
==Project Description==
 
==Project Description==
Line 23: Line 26:
 
|
 
|
 
<!-- Approach and Plan bullet points -->
 
<!-- Approach and Plan bullet points -->
−
* TBD
+
* Breakout session in Kiva room at 12PM on Wednesday
 
|
 
|
 
<!-- Progress and Next steps bullet points (fill out at the end of project week) -->
 
<!-- Progress and Next steps bullet points (fill out at the end of project week) -->
−
*
+
* About 30 participants. Presentation + demo + discussion
 +
* Basics of the underlying Segmentations infrastructure presented (Csaba): [https://www.slicer.org/w/images/6/64/20160526_Segmentations.pptx these slides] ([https://www.slicer.org/w/images/a/ae/20160526_Segmentations.pdf PDF]) (This is a longer version of the slides presented. More information on the [https://www.slicer.org/wiki/Documentation/Nightly/Modules/Segmentations 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==
 
==Background and References==
 
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data -->
 
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data -->
 +
 +
== 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

Latest revision as of 19:16, 16 January 2017

Home < 2017 Winter Project Week < ImprovementsToSegmentEditor

  • Highlights of segmentations 1

  • Highlights of segmentations 2

  • 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

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
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