1. ter Haar Romeny, FEV Application of Gaussian curvature: Automatic colon polyp detection in virtual endoscopy

2. ter Haar Romeny, FEV MIT AI Lab The shape index is a sensitive measure for surface shapes

3. ter Haar Romeny, FEV Enhancement by Gaussian curvature PMS CT slice with tagged residual sticking to the wall Same slice after electronic cleansing Philips MS Electronic colon cleansing

4. ter Haar Romeny, FEV Current visualization Normal dose Smooth surface Low dose Blobs appear Normal dose Rough surface

5. ter Haar Romeny, FEV Proposed solutions Bilateral filtering  blobs Gradient smoothing  rough surface

6. ter Haar Romeny, FEV Results: normal dose

7. ter Haar Romeny, FEV Results: all dose levels 1.6 mAs 6.25 mAs64 mAs

8. ter Haar Romeny, FEV Enhancement and detection of micro-vasculature: Cryo-microtome images of the goat heart Very high resolution: about 40×40×40 µm; Continuous volume Huge stacks (billions of voxels, millions of vessels) Strange PSF in direction perpendicular to slices Scattering Broad range of vessel sizes and intensities. 8 cm = 2000 pixels MSc thesis Edwin Bennink, 2007

9. ter Haar Romeny, FEV The Cryomicrotome Coronary arteries of a goat heart are filled with a fluorescent dye; Cryo: The heart is embedded in a gel and frozen (-20°C); Microtome: The machine images the sample’s surface, scrapes off a microscopic thin slice (40 μm), images the surface, and so on … a.b.

10. ter Haar Romeny, FEV Original data

11. ter Haar Romeny, FEV Dark current noise

12. ter Haar Romeny, FEV Noise subtracted from data

13. ter Haar Romeny, FEV Frangi’s vessel-likeliness Original data (normal and log-scale) (The images are inverted)

14. ter Haar Romeny, FEV Center line detection Center line smoothing Center line 3D view

15. ter Haar Romeny, FEV Canceling transparency artifacts Point-spread function in z-direction (perpendicular to slices)

16. ter Haar Romeny, FEV Canceling transparency artifacts Point-spread function in z-direction (perpendicular to slices)

17. ter Haar Romeny, FEV Canceling transparency artifacts Point-spread function in z-direction (perpendicular to slices)

18. ter Haar Romeny, FEV Canceling transparency artifacts Point-spread function in z-direction (perpendicular to slices)

19. ter Haar Romeny, FEV Canceling transparency artifacts Point-spread function in z-direction (perpendicular to slices)

20. ter Haar Romeny, FEV Canceling transparency artifacts The effect of transparency is theoretically a convolution with an exponent; s denotes the tissue’s transparency. - 6 - 4 - 224 z 0.2 0.4 0.6 0.8 1 f(z)f(z)

21. ter Haar Romeny, FEV Canceling transparency artifacts In the Fourier domain; The solid line is the real part, the dashed line the imaginary part.

22. ter Haar Romeny, FEV Canceling transparency artifacts The new 0 th order Gaussian filter k(z) (in z-direction) becomes: - 4 - 224 z 0.1 0.2 0.3 0.4 0.5 k(z)(z)

23. ter Haar Romeny, FEV Canceling transparency artifacts Solution to the problem: embed this property in the (Gaussian) filters by division in the Fourier domain; Multiplication is convolution, thus division is deconvolution.

24. ter Haar Romeny, FEV Canceling transparency artifacts z x Default Gaussian filters Enhanced Gaussian filters

25. ter Haar Romeny, FEV Extract vasculature with ‘vesselness’ From T1w MRI with contrast Frangi’s vesselness measure [Frangi et al., 1998] Enhance tubular structures while reducing other morphologies E. Brunenberg, MSc project 600104.SS

26. ter Haar Romeny, FEV Vesselness: Vessel enhancement filtering Better delineation of small vessels Preprocessing before MIP Preprocessing for segmentation procedure Frangi, W. J. Niessen, K. L. Vincken, and M. A. Viergever. Multiscale vessel enhancement filtering. In Proc. 1st MICCAI, pages 130-137, 1998.

27. ter Haar Romeny, FEV Vesselness The second order structure is exploited for local shape properties

28. ter Haar Romeny, FEV

29. Deviation of a plate-like structure: Similarity to blob-like structure: Frobenius norm, second-order-like structure:

30. ter Haar Romeny, FEV In the definition of vesselness the three properties are combined: 1 >0  2 >0 : only bright structures are detected; ,  and c control the sensitivity for  A,  B and S; Frangi uses  = 0.5,  = 0.5, c = 0.25 of the max intensity.

31. ter Haar Romeny, FEV Abdominal MRA Maximum intensity projection No 3D information Overlapping organs

32. ter Haar Romeny, FEV 2D Example: DSA

33. ter Haar Romeny, FEV Scale integration:

34. ter Haar Romeny, FEV Closest Vessel Projection

35. ter Haar Romeny, FEV Trabecular Bone Analysis Bone appears in two forms Cortical Bone Trabecular Bone connected network of rods & plates loading dependent architecture

36. ter Haar Romeny, FEV Stress routes Wolff’s Law “The internal structure and external shape of a bone develop in response to the change in function and forces acting upon it” Culman Meyer “Trabecular pattern is oriented with routes of stress”

37. ter Haar Romeny, FEV Clinical Relevance Trabecular Architecture important parameter in bone strength (clinically proven) Applications for in vivo analysis determine fracture risk monitoring structure in aging monitor degree and development of osteoporosis (treatment available) monitoring malgrowth near epiphyses placing implants and evaluating receipt

38. ter Haar Romeny, FEV

39. Stress Routes in Ankle

40. ter Haar Romeny, FEV MR Ankle, FFE, short TE (300  m)

41. ter Haar Romeny, FEV CT dry femur (250  m)

42. ter Haar Romeny, FEV Structural Information

43. ter Haar Romeny, FEV 3D orientaties

44. ter Haar Romeny, FEV Dominant orientations Orientations preferentially along anatomical axis Histogram of 3D directions: