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Stereology

Stereology. More Applications and Examples of Programs for Algorithms. Goals of This Project Were…. Find a Program that develops 3-D Images from Stereological Images Try to find algorithms for the reconstruction of such images Reference Sites to increase the database for class research.

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Stereology

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  1. Stereology More Applications and Examples of Programs for Algorithms

  2. Goals of This Project Were… • Find a Program that develops 3-D Images from Stereological Images • Try to find algorithms for the reconstruction of such images • Reference Sites to increase the database for class research

  3. Limitations of the Project • Was difficult to find algorithms for reconstruction • For many demos performance machines were needed; SGI/Sun stations • Some of the sites had broken links to their demos • If wanted to buy, the programs were $$

  4. Definition of Stereology • A body of mathematical methods relating three dimensional parameters defining the structure, to two dimensional measurements obtainable on sections of the structure • Statistical in nature, as it is random where intersection occurs • Handout on introduction to Stereology

  5. Reference Sites • http://www.3dcounting.html/ • http://www.stereologer.com/Stereo_Exec.html • http://www.ssrecn.html • http://www.phtshp.htm/ • http://www.confocl.htm/ • http://www.ippage.htm/ • http://www.index.html/

  6. Image Pro Express • Developed by Media Cybernetics • Easier interface for measurements, such as the length/angles and profiles of the image • Photoshop like nature • However it was easier to overlay images • Meant to import digital camera and scanner images

  7. Red to Blue Blue to Red Image Pro Express Cont.

  8. Voxtool 1.0.4 • Segmentation is done through lower and higher HU-thresholds • Shaded surface display, MIP, RaySum, Integral and Multiplanar reformatting (MPR) as well as movie loop (if memory permits full 360 degree rotation with 6 degree intervals is sometimes possible)

  9. Image Pro Measurements

  10. Image Pro Measurements 2

  11. Measurements 2 B

  12. Measurements 3

  13. Voxtool Cont. • Select/remove object, filter floaters (user-definable size), scalpel (user-definable cut depth), erosion, dilation, open bridges and close gaps-functions • Intersection, union, difference and delta-functions between manipulated models

  14. Voxtool Example

  15. Voxtool Example 2

  16. Volpack Software • Developed by Philippe Lacroute and Marc Levoy, Fast Volume Rendering Using a Shear-Warp Factorization of the Viewing Transformation • Better algorithm, because it achieves its speed by exploiting coherence in the volume data and the intermediate image

  17. Volpack Cont. • They introduce a data structure for encoding spatial coherence in unclassified volumes (i.e. scalar fields with no precomputed opacity) • This was linked through the sites researched, and provides information for how reconstruction is being improved

  18. Volpack Cont. • A volume is simply a 3D array of data. The type of data can be almost anything, but if you choose to use the classification and shading routines provided by VolPack then you must supply the fields these routines require. You may also wish to precompute information required by your shader or classifier and store it in the voxel. Here is an example layout for a voxel:

  19. Example Code for Volume Calc typedef unsigned char Scalar; typedef unsigned short Normal; typedef unsigned char Gradient; typedef struct { Normal normal; Scalar scalar; Gradient gradient; } Voxel;

  20. Explanation In this example the data stored in a voxel includes an 8-bit scalar value and two precomputed fields. The first precomputed field is a surface normal vector encoded in a 16-bit field; this field is used by VolPack's shading routines. The second precomputed field is the gradient-magnitude of the scalar value; this field can be used for detecting surface boundaries during classification

  21. Explanation 2 • This is a one of many software programs (both commercial and otherwise) available for 3D reconstruction of MRI, CT, confocal, and serial-section data for medical/life-sciences imaging.

  22. Stereological Slices

  23. Stereological Image

  24. More Information • http://www.vp_userguide.html/ • Explanations for users guide • The creator has also written a book

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