EE549
Biomedical
Image Analysis
Meeting times : Tuesday 9:45, 10:45, 11:45
Instructor : Bilge Karaçalı, PhD
Office : EEE Building Room 209
Phone : 6719
E-mail : bilgekaracali@iyte.edu.tr
Summary
Bioimaging in histopathology. Digitized histologic slides: sectioning of tissue samples, immunohistochemical staining, image acquisition. Preprocessing of histology image data. Tissue segmentation. Region segmentation. Segmentation and morphological characterization of cell nuclei. Abnormality detection via pattern classification. Analysis of three-dimensional radiological sequences. Format conversion and preprocessing. Co-registration and lesion detection. Computational anatomy via deformable registration. Comparative group studies: statistical parametric mapping, high-dimensional pattern recognition. Computational anatomy in four dimensional sequences.
Grading
Midterm 20%
Final 20%
Homework 30%
Project 30%
Material
Course Notes
Week 1: Overview of histology image data
Week 2: Grayscale tissue segmentation
Week 3: Color tissue segmentation
Week 4: Nuclei detection and morphological characterization
Week 5: Abnormality detection
Week 6: Overview of radiological sequences
Week 7: Probabilistic lesion detection
Week 8: Non-parametric lesion detection
Week 9: Anatomical atlases for computational anatomy
Week 10: Deformable image registration
Week 11: Shape representations for morphological analysis
Week 12: Comparative group studies using Voxel-Based Morphometry
Week 13: Comparative group studies based on machine-learning
Week 14: Computational anatomy in four dimensions
Homework
Homework 1 (due 13/03/2012)
Homework 2 (due 8/5/2012)
Homework 3 (due 25/5/2012)
Tests
Data files
