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Anisotropic Diffusion’s Extension to Constrained Line Processes Anisotropic Diffusion’s Application in 3D Confocal Microscopy Image Processing. Cédric Dufour. Contents. Anisotropic diffusion’s basics Extension to constrained line processes
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Anisotropic Diffusion’s Extension toConstrained Line ProcessesAnisotropic Diffusion’s Application in3D Confocal Microscopy Image Processing Cédric Dufour
Contents • Anisotropic diffusion’s basics • Extension to constrained line processes • Anisotropic diffusion vs. constrained line processes • 3D microscopy image processing • Conclusions
Grayscale intensity value Diffusion coefficient Time (iteration) variable Anisotropic diffusion’s basics (1) • Underlying principle: standardheat diffusion • Equivalent to gaussian local meaning(the variance being related unequivocally to the diffusion coefficient)
Anisotropic diffusion’s basics (2) • Problem: diffusion occurs in all direction, regardless of edges • Blurring
Anisotropic diffusion coefficient(“edge stopping” function) Anisotropic diffusion’s basics (3) • Solution: bind the diffusion coefficient to the gradient of the intensity • Care must be taken in the choice of the edge stopping function for the problem to be well-posed More info: edge stopping function
A.D. Anisotropic diffusion’s basics (4) • Results: diffusion is inhibited when the gradient gets more important (edges) • Piecewise smooth image
Smoothness functional Smoothness norm Extension to constrained line processes (1) • Anisotropic diffusion can be derived from the minimization of a smoothness functional: More info: 3D neighborhood for anisotropic diffusion
Line process Spatial constraints Fitting constant Line process penalty function Extension to constrained line processes (2) • Expressing this minimization problem according to the line process formulation, we have: • Adding explicit spatial constraints: More info: line process and penalty function characteristics
Extension to constrained line processes (3) • The line process formulation is related to the standard anisotropic formulation through: More info: starting relating axiom between the standard anisotropic formulation and the line process formulation
Extension to constrained line processes (4) • Computational results: Image Gradient
Hysteresis term Non-maximum suppression term Extension to constrained line processes (5) • Adding spatial constraints... • … we obtain the following iterative formula: More info: spatial constraints clique
C.L.P. Extension to constrained line processes (6) • Results: the diffusion is inhibited by the spatial constraints • Sharper details and smoother contours
A.D. C.L.P. C.L.P. A.D. Anisotropic diffusion vs. constrained line processes (7) • Comparative MSE and variance: MSE Variance
3D microscopy image processing (1) • Goal: obtain correlation statistics in multi-channel 3D confocal microscopy images CH.1 CH.2
3D microscopy image processing (2) • Step 1: de-noising (using anisotropic diffusion) • Smooth image CH.1 CH.2
3D microscopy image processing (3) • Step 2: thresholding • Proteins mask CH.1 CH.2
3D microscopy image processing (4) • Step 3: skeleton and labeling • Disjointed protein labeled skeleton CH.1 CH.2 More info: disjointed clusters
3D microscopy image processing (5) • Step 4: geodesic growth • Disjointed protein labeled mask CH.1 CH.2
3D microscopy image processing (6) • Step 5: compute distance table • Distance between proteins CH.1 CH.2
3D microscopy image processing (7) • Step 6: clustering • Group proteins according to the separating distance D = 5 x ‘mean size’ D = 7.5 x ‘mean size’
3D microscopy image processing (8) • Step 7: compute the statistics • Proper correlation statistics and interpretation To do! (IBCM’s biologists task)
Conclusions • Anisotropic diffusion is a powerful tool for de-noising • Spatial constraints (added through the line process formulation) allow to obtain better quality denoising • Application of the anisotropic diffusion along with other morphological and clustering tools allowed efficient segmentation and classification of proteins appearing in 3D confocal microscopy images.