A 3D Intensity Model Based on Spherical Harmonics for Automatic 3D - PowerPoint PPT Presentation

ISBI 2013 Redux Presentation . A 3D Intensity Model Based on Spherical Harmonics for Automatic 3D Segmentation of Heterochromatin Foci . Simon Eck, Karl Rohr, Andreas Biesdorf, Katharina Muller-Ott, Karsten Rippe and Stefan Worz Institute: University of Heidelberg, Research Group Genome Organization & Function, Germany May 5, 2013 ISBI 2013 Redux Presentation . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. . .. . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 1 / 1

ISBI 2013 Redux Presentation A 3D Intensity Model Based on Spherical Harmonics for Automatic 3D Segmentation of Heterochromatin Foci Analytic representation of star-shaped foci. Figure : Heterochromatin in a Cell Nucleus in 3D Microscopy . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 2 / 1

ISBI 2013 Redux Presentation A 3D Intensity Model Based on Spherical Harmonics for Automatic 3D Segmentation of Heterochromatin Foci √  2 N ( l , m ) P m l (cos θ ) cos m ϕ m > 0     N ( l , 0) P m l (cos θ ) m = 0 Y lm = √  2 N ( l , | m | ) P | m | (cos θ ) cos | m | ϕ m < 0   l  L l √ ∑ [ a 0 l N 0 l P 0 ∑ ( a m l cos m ϕ + b m 2 N m l P m r SH = l (cos θ ) + l sin m ϕ l )(cos θ )] l =0 m =1 { 1 0 ≤ r ≤ r SH g SH ,σ ( r , θ, ϕ ) = G σ ∗ 0 else v ) = Img BG + ( Img FG − Img BG ) g SH ,σ ( r , θ, ϕ, θ ′ ) g SH ,σ ( r , θ, ϕ,⃗ ∫ v ) − Img ( r , θ, ϕ )) 2 min E = min ( g SH ,σ ( r , θ, ϕ,⃗ ROI . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 3 / 1

ISBI 2013 Redux Presentation . 3D Haar-like Elliptical Features for Object Classification in Microscopy . Fernando Amat and Philipp J.Keller Howard Hughes Medical Institute, Virginia, USA May 5, 2013 ISBI 2013 Redux Presentation . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. . .. . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 4 / 1

ISBI 2013 Redux Presentation 3D Haar-like Elliptical Features for Object Classification in Microscopy . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 5 / 1

ISBI 2013 Redux Presentation . Detection of Symmetric Junctions in Biological Images Using 2D Steerable Wavelet Transforms . Zsuzsanna Puspoki, Cedric Vonesch and Michael Unser Ecole Polytechnique Federale de Lausanne, Switzerland May 5, 2013 ISBI 2013 Redux Presentation . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. . .. . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 6 / 1

ISBI 2013 Redux Presentation Detection of Symmetric Junctions in Biological Images Using 2D Steerable Wavelet Transforms . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 7 / 1

ISBI 2013 Redux Presentation . Microvasculature Network Identification in 3D Fluorescent Microscopy Images . Sepideh Almasi and Eric L.Miller Tufts University, USA May 5, 2013 ISBI 2013 Redux Presentation . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. . .. . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 8 / 1

ISBI 2013 Redux Presentation Microvasculature Network Identification in 3D Fluorescent Microscopy Images . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 9 / 1

ISBI 2013 Redux Presentation Microvasculature Network Identification in 3D Fluorescent Microscopy Images m n ∑ ∑ min E = arg max α l e l + β k v k (1) e l , v k l =1 k =1 e l , v k ∈ { 0 , 1 } , δ ( e l , v k ) = 1 (2) s.t. l = 1 , 2 , ..., m ; k = 1 , 2 , ..., n (3) || Il || 1 λ △ ω ( || Il || 1 ) − ˆ dl )( e α l = H χ ( e σ l − ϕ l ) (4) dl cl k ∑ β k = − ( σ k + θ ) (5) l =1 . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. .. . . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 10 / 1

ISBI 2013 Redux Presentation Conclusion . . 1 A 3D Intensity Model Based on Spherical Harmonics for Automatic 3D Segmentation of Heterochromatin Foci . . 2 3D Haar-like Elliptical Features for Object Classification in Microscopy . . 3 Detection of Symmetric Junctions in Biological Images Using 2D Steerable Wavelet Transforms . . 4 Microvasculature Network Identification in 3D Fluorescent Microscopy Images . . . . . . . . . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . .. . .. . . .. . .. .. . .. . .. . .. . .. . .. . .. . .. . .. . .. . Mengliu Zhao MIAL May 5, 2013 11 / 1