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Biomedical Image Analysis and Machine Learning
BMI 731 Winter 2005 Kun Huang
Department of Biomedical InformaticsOhio State University
- Introduction to biomedical imaging
- Imaging modalities
- Components of an imaging system
- Areas of image analysis
- Machine learning and image analysis
- Why imaging? - Diagnosis
X-ray, MRI, Ultrasound, microscopic imaging (pathology and histology) …
- Visualization (invasive and noninvasive)3-D, 4-D
- Functional analysisFunctional MRI
- PhenotypingMicroscopic imaging for different genotypes, molecular
imaging
- QuantificationCell count, volume rendering, Ca2+ concentration …
- Imaging modalities- Wavelength
- Electron microscope- X-ray- UV- Light- Ultrasound
- MRI- Fluorescence- Multi-spectral- Tomography- Video
Ultrasound
- Components of Imaging System- Instrumentation :
- Electrical engineering, physics, histochemistry …
- Image generation- Sensor technology (e.g., scanner), coloring agents …
- Image processing and enhancement- Both software, hardware, or experimental (dynamic
contrast)
- Image analysis at all levels- Image processing, computer vision, machine learning- Manual/interactive
- Image storage and retrieval- Database/data warehouse
- Areas of Image Processing and Analysis- Image enhancement
- Color correction, noise removal, contrast enhancement …
- Feature extraction- color, point, edge (line, curves), area- cell, tissue type, organ, region
- Segmentation- Registration- 3-D reconstruction- Visualization- Quantization
- Image Analysis and Machine Learning- Why machine learning
- Classification at all levels- Pixel, texture, object …
- Pattern recognition, statistical learning, multivariate analysis …
- Statistical properties
Curtersy of Raghu Machiraju
- Common machine learning techniques- Dimensionality reduction
- Principal component analysis (PCA, SVD, KLT)- Linear discriminant analysis (LDA, Fisher’s discriminant)
stackPCA
- Common machine learning techniques- Supervised learning
Learning algorithm
Classifier ?
- Neural network, Support vector machine (SVM), MCMC, Bayesian network …
- Common machine learning techniques- Unsupervised learning
- K-means, K-subspaces, GPCA, hierarchical clustering, vector quantization, …
- Dimensionality Reduction- Principal component analysis (PCA)
- Singular value decomposition (SVD)- Karhunen-Loeve transform (KLT)
Basis for P SVD
- Dimensionality Reduction- Principal component analysis (PCA)
=
=
- Dimensionality Reduction- Principal component analysis (PCA)
=
≈
Knee point
Optimal in the sense of least square error.
- Principal Component Analysis (PCA)- Geometric meaning
- Fitting a low-dimensional linear model to data
Find µ and E such that J is minimized.
- Principal Component Analysis (PCA)- Statistical meaning
- Direction with the largest variance
- Principal Component Analysis (PCA)- Algebraic meaning
- Energy
- Principal Component Analysis (PCA)- Application : face recognition (Jon Krueger et. al.)
Average face
Eigenfaces – Principal Components
- Linear Discriminant Analysis
B
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(From S. Wu’s website)
Linear Discriminant AnalysisB
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.(From S. Wu’s website)
- Linear Discriminant Analysis (PCA)- Which direction is a good one to pick?
- Maximize the inter-cluster distance- Minimize the intra-cluster distance
- Compromise : maximize the ratio between the above two distances
- Next time- Supervised learning - SVM- Unsupervised learning – K-means- Spectral clustering
OR
- CT, Radon transform backprojection- MRI- Other image processing techniques (filtering,
convolution, color and contrast correction …)