3D Image Analysis

Type:	Spezialvorlesung
Credits:	2+2 SWS, 6 ECTS
Lecture by:	Junior-Prof. Olaf Ronneberger
Time and Location:	Lectures: Tuesday, 10hct-12h, Room: Building 052, HS 02-017 Exercises: Friday, 10hct-12h, Room: Building 082, Pool 00-029 (Start at Fri., 8.05.2015)
Language:	Slides: English, Spoken language: English / German (nach Wunsch der Teilnehmer)
Exercises by:	Benjamin Drayer and Benjamin Ummenhofer

Overview

This course will introduce the basic concepts and techniques that are used in analysis of 3D images (volumetric data sets). The focus will be on data sets that are recorded in the biomedical research.

The exercises will focus on practical applications of the concepts, efficient 3D data handling and processing in C++, common libraries and tools in this area. The students are expected to write small programs, that solve given 3D image analysis tasks.

Prerequisites

Kursvorlesung Image Processing and Computer Graphics
Programming skills (preferably in C++)

Lectures

(contents will be updated during semester)

Number	Date	Topic	Slides
1	Fri, 24.04.2015	Introduction	01_Introduction.pdf vorlesung_3dia_01.mp4 (251MB) (sorry, broken audio)
2	Tue, 28.4.2015	Intensity Based Registration Registration Introduction Intensity based Registration (Transformation models, Similarity Measures)	02_Registration_Introduction.pdf vorlesung_3dia_02.mp4 (134MB)
3	Tue, 12.5.2015	Feature Based Registration Optimizers for Intensity Based Registration Point Based Registration with Known Correspondencies (Umeyama) Feature Based Registration with Unknown Correspondecies (ICP) Fast search for closest point: KD Trees	03_Feature_based_registration.pdf umeyama.pdf vorlesung_3dia_03.mp4 (119MB)
4	Tue, 19.5.2015	Feature Based Registration (cont.) Fast search for closest point: Distance Transforms Fast Euclidean distance transform from Felzenszwalb Variational Deformable Registration (1) Deformable Registration Introduction Notation Energy Functional	04_Feature_based_registration2+deformable_registration1.pdf vorlesung_3dia_04.mp4 (119MB)
5	Tue, 2.6.2015	Variational Deformable Registration (cont.) Energy Functional Gradient of a Functional Gradient of the Smoothness term Euler-Lagrange Equations	05_Deformable_Registration.pdf vorlesung_3dia_05.mp4 (116MB)
6	Tue, 9.6.2015	Deformable Registration (cont.) Optimization Grid-based Registration using FFD's Combinatorial Optimization	06_Deformable_Registration_cont.pdf vorlesung_3dia_06.mp4 (129MB)
7	Tue, 16.6.2015	Diffeomorphic Registration Displacement fields vs. Diffeomorphisms Generation constant velocity field variable velocity field EMPIRE 10 Grand Challenge Datasets Challenge Setup Results The Best Performing Algorithms	07a_Diffeormorphism.pdf 07b_Empire_Challenge.pdf vorlesung_3dia_07.mp4 (160MB)
8	23.6.2015	Detection and Feature Extraction SIFT	08_Detection_and_Feature_extraction.pdf vorlesung_3dia_08.mp4 (151MB)
9	30.6.2015	Rotation Invariance 2D Fourier series Shift theorem Rotation invariant features Computation in the image domain	09_Fourier_Features.pdf vorlesung_3dia_09.mp4 (131MB)
10	7.7.2015	3D Rotation Invariance Spherical Harmonics Rotation of functions on a sphere Rotation invariant descriptors Polar and spherical tensor algebra	10+11_Spherical_Harmonics+HOG.pdf vorlesung_3dia_10.mp4 (142MB)
11	14.7.2015	Rotation Invariant HOG (2D+3D) From discrete HOG to continuous orientation distribution function Polar and spherical tensor algebra From HOG cells to HOG descriptors Application ViBE-Z: Virtual Brain Explorer for Zebrafish	10+11_Spherical_Harmonics+HOG.pdf 11_ViBE-Z.pdf vorlesung_3dia_11.mp4 (153MB)
12	21.7.2015	Application (cont.) ViBE-Z: Virtual Brain Explorer for Zebrafish (cont.) Summary and questions	vorlesung_3dia_12.mp4 (66MB)

Exercises

Number	Date	Topic	Exercise / Additional Material	Sample Solution
1	Fri, 8.05.2015 Due date: 12.05.2015	Quick Introduction Maximum and average intensity projections	01_Introduction_quick.pdf Exercise_01.pdf whatisit_124x216x181_8bit.raw	slices.cc mip.cc aip.cc
2	Fri, 15.05.2015 Due date: 22.05.2015	Rotating videos of 3D images Anaglyph Videos 3D Videos of Today	Exercise_02.pdf test.cc Artemisia_pollen_71x136x136_8bit.raw Zebrafish_71x361x604_8bit.raw	updated 2015-06-11 render_pollen_movie.cc render_zebrafish_movie.cc render_pollen_anaglyph_movie.cc render_zebrafish_anaglyph_movie.cc render_zebrafish_3d_movie.cc render_zebrafish_3d_movie_highres.cc
3	Fri, 22.05.2015 Due date: 09.06.2015	Rigid Registration	Exercise_03.pdf leaf_t5_150x521x396_8bit.raw leaf_t6_150x521x396_8bit.raw	updated 2015-06-11 rigid_registration.cc rigid_registrationCOM.cc
4	Fri, 12.06.2015 Due date: 23.06.2015	Landmark based Registration with the Umeyama Method	Exercise_04.pdf my_blitz.hh, BlitzHDF5Helper.hh, BlitzHDF5Helper_test.cc zebrafish0.h5, zebrafish1.h5 vivi (hdf5 viewer software) References: [1] Umeyama, [2] SVD	common.h, umeyama.cc
5	Fri, 26.06.2015 Due date: 07.07.2015	Dense Elastic Registration	Exercise_05.pdf square.h5, circle.h5, smile1.h5, smile2.h5, zebra1.h5, zebra2.h5, Fast_PD.tar.gz FlowToImage.hh	elastic.cc
6	Fri, 10.07.2015 Due date: 21.07.2015	Transform the World	Exercise_06.pdf world_elevation.h5	compute_basis.cc transform_world.cc

Please mail your solutions (only the C++ - files) to
and
and CC to ronneber@informatik.uni-freiburg.de

last changed: 2015-07-22 by Benjamin Ummenhofer