1 / 61

mipav.cit.nih

http://mipav.cit.nih.gov. Segmentation and Annotation of Medical Images with MIPAV. Justin Senseney SenseneyJ@mail.nih.gov dcb.cit.nih.gov/~ senseneyj Biomedical Image Processing Research Services Section Center for Information Technology mipav.cit.nih.gov. MIPAV Team. Employees

yadid
Download Presentation

mipav.cit.nih

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. http://mipav.cit.nih.gov

  2. Segmentation and Annotation of Medical Images with MIPAV Justin Senseney SenseneyJ@mail.nih.gov dcb.cit.nih.gov/~senseneyj Biomedical Image Processing Research Services Section Center for Information Technology mipav.cit.nih.gov

  3. MIPAV Team Employees Ruida Cheng William Gandler Matthew McAuliffe Evan McCreedy Justin Senseney Fellows Sara Shen Contractors Alexandra Bokinsky, Geometric Tools Inc. (Visualization) Olga Vovk, SRA International Inc. (Technical Writing) Alumni Paul Hemler, Agatha Munzon, Nishith Pandya, Beth Tyriee, Hailong Wang

  4. Agenda • Review • VOI • Creation • Manipulation • Masks • Creation • Conversion • Morphological operators (2D and 3D) • Paint • Creation • Fill • Segmentation • Fuzzy C-means • Level set • Thresholding • Watershed • Segmentation • Watershed

  5. Review • MIPAV as collaboration tool • Opens all image formats • Scriptable • Quantitative and qualitative

  6. VOI Volume of interest

  7. Agenda • VOI (Volume of interest) • Definition • Creation • Annotations • Points • Lines • Curves • Cube • Manipulation • Split • Undo/Redo • Cut/Copy/Paste • Propagation

  8. VOI • Volume of interest – one or more contours on an image

  9. Annotation • Save names and notes • Place in text location, move arrow

  10. Point • Shift for multiple points • Delete removes, renumbers to keep consecutive • Can move

  11. Line • Right click to show options • Intensity plot from green point

  12. Protractor • Initial point is intersection of two lines • Draw outwards • Re-click to • orient angle

  13. Square • Start with any corner, drag in any direction • To modify, click a point, becomes “active” VOI.

  14. Circle • Start at circle center • Drag entire shape

  15. Polyline/polygon • Shape can be open

  16. Levelset • Looks for closest intensity value • Topographic map • Once active, alt+hold down mouse • to modify boundary.

  17. Livewire • Larger changes in magnitude with smaller distance. • Minimum cost

  18. Cube • “0” is always the initial curve • Numbering does not indicate slice

  19. Split • Splits into same VOI, different contour • Each contour is closed • Multiple VOIs split • Multiple contours split

  20. New VOI • Open/closed VOIs cannot be combined • Statistics

  21. Quiz • Manual VOI change using ALT+hold down mouse. Which direction is required? • A. clockwise • B. counter-clockwise Answer: Both, but choose one each time

  22. Undo/Redo • Applies to VOI operations only • Keyboard shortcut: Ctrl+Z (Undo), Ctrl+Y (Redo)

  23. Cut/Copy/Paste • Cut – delete, store to paste • Copy – store to paste • Paste – Place active VOI in current slice of active image

  24. Propagate • Down one slice • Up one slice • To all slices

  25. And • Default is in place

  26. Fill • Fills with zeros

  27. Evolve Boundary • Active contour • Combine with propagation to adjacent slices • Small Gaussian sensitive to noise

  28. Interpolate • Define contours on non-contiguous slices • Contours part of same VOI • Must be selected Slice 86 Slice 89 Slice 95

  29. Break

  30. Mask Defined on pixels

  31. Create new mask

  32. Open/Save mask

  33. Conversion VOI menu options

  34. AND Mask operation Performs actual conversion

  35. Morphology

  36. Mathematical Morphology • Erosion • Dilation • Opening • Closing • Distance maps

  37. Mathematical MorphologyOpening Structuring Element Source object Erosion 2D 3x3 structuring element Dilation 3D 3x3x3 structuring element Result: Erosion + Dilation = Opening

  38. Mathematical MorphologyClosing Structuring Element Source object Dilation Result: Dilation + Erosion = Closing Erosion

  39. Original boundary Result Erode Erode Dilate Dilate Opening Closing Mathematical MorphologyNoise Removal Input

  40. Distance transform Object distance - minimum Euclidian distance from any edge to a point interior to the object Background distance - minimum Euclidian distance from any edge to a point exterior to the object (i.e. background)

  41. Paint Defined on masks

  42. Brush

  43. Advanced Paint

  44. Region Grow

  45. Erasers

  46. Propagation • Same as VOI options • No active contour solution

  47. Paint brush options • Brush size • Brush pattern • Brush intensity

  48. Paint display options • Select color • Change opacity • Show border

  49. Mask options • Just like VOI mask options, another conversion tool

  50. Undo paint • Only applies to paint • Does not change masks

More Related