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Feature-Based Classification of Mouse Eye Images

Feature-Based Classification of Mouse Eye Images. Jenny Yuen, Yi Li, and Linda Shapiro. This work is sponsored by the NIH Interdisciplinary Center for Structural Informatics. National Library of Medicine under grant No. P20 LM007714. Problem. “…A cataract is a clouding of the eye's lens.”

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Feature-Based Classification of Mouse Eye Images

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  1. Feature-Based Classification of Mouse Eye Images Jenny Yuen, Yi Li, and Linda Shapiro This work is sponsored by the NIH Interdisciplinary Center for Structural Informatics. National Library of Medicine under grant No. P20 LM007714

  2. Problem • “…A cataract is a clouding of the eye's lens.” • The University of Michigan Kellogg Eye Center • There are ideas associating them to other illnesses. • Different cataracts have different effects, so the classification of cataracts is important. • The classification is currently done manually through an expert. • This involves a lot of time and knowledge of the area.

  3. Problem Statement - Eye Image Center of the eye cornea cornea Center of the eye

  4. Problem Statement(1) • We are given a set of cataract categories S = {C1, C2, …, Cn}. Control Schwann Cell I factor knockout Secreted Protein Acidic and Rich Cystene knockout CP115 knockout Alpha A-Crystallin knockout

  5. Proposed solution • Automate the classification. Control Classifier SPARC SCI

  6. Training Data • For each cataract category, we are given a set of mouse eye images that have such cataract. Control Schwann Cell I factor knockout Secreted Protein Acidic and Rich Cystene knockout CP115 knockout Alpha A-Crystallin knockout

  7. Problem Statement • We are given: • S = {C1, C2, …, Cn} classes of cataracts and for each class Ci: • A set of mouse eye training images exhibiting the corresponding cataract. • A test image I that is not in the training set. • We want: • A classifier that can determine the class CI, to which I belongs.

  8. Approach • Feature Detection • Ring Extraction • Intensity Curve • Texture • Eye Center Appearance • Training

  9. Ring Detection • For each pixel, apply a local equalization on a window of 3x3 (for edge enhancement). Before local equalization After local equalization

  10. Ring Detection (2) • Take a horizontal axis x that passes through the middle of the image (row nrows/2). • For each pixel p(x,xi) in row x, 1)Take the region of the image in the circular sector Ci with center p(x,xi) and central angle q. 2) Map this circular sector to a rectangle R using a polar coordinate transformation. 3) Represent each column of R by its average intensity. 4) Compute the variance of the intensities in this curve. This is the score for p(x,xi).

  11. Ring Feature Extraction 1 2 score 4 3

  12. Ring Detection (3) • Let Lbest be the curve to which the circular sector with the highest score was mapped. • Create a feature vector with the following information from Lbest: • Number, mean, and variance of maxima. • Number, mean, and variance of minima. • Mean and variance for the distance between every two consecutive maxima. • Mean and variance for the distance between every two consecutive minima.

  13. y z x Intensity Curve Feature • The intensity curve of a line through the center of the eye with respect to the plane described by the image.

  14. Intensity Curve(2) • Let P = {p| p is a pixel in the row r/2 in the image I} • Fit a polynomial on the function C: • C(x) = {Intensity(I(r/2,x))} • Call this polynomial fit on C FitC.

  15. Curvature Description(3) • We could use the coefficients of FitC as features to describe each class. • But there is a problem: Noise in the image might affect the polynomial. • Solution: Use the Fourier Transform

  16. Intensity Curve(4) – Modified Algorithm • Let P = {p| p is a pixel in the row r/2 in the image I} • C(x) = {Intensity(I(r/2,x))} • Apply a Fourier Transform to C: Fourier(C). • Fit a polynomial on Fourier(C). Call this polynomial fitting FitFourier(C). • Use the coefficients of FitFourier(C) as features.

  17. Intensity Curve(5) With the application of a Fast Fourier Transform Intensity values {coeff1Real, coeff1Im , coeff2Real, coeff2Im, coeff3Real, coeff3Im, coeff4Real, coeff4Im}

  18. Eye Center Appearance • Some of the classes have a cloudy circular region in the center of the eye. • We plan to identify these, extract features such as the size and intensity of the region, and use this information for classification.

  19. Training • Using the features from a training set, we can input this data in a neural net. (f1,f2, …. fn) test image vector (f11, f12, …. f1n, C1) (f21, f22, …. f2n, C2) . (fk1, fk2, …. fkn, Ck) neural net Classification training data

  20. Preliminary Results on 3 Classes Predicted Actual

  21. Confusion between images • Some of the images are so similar to each other that it is very hard, even for an expert, to determine the class. There are 50 of these. WT SPARC

  22. Continued Work • Retrain and retest without the ambiguous images. • Try more features separately. • Try combinations of features. • Try other classifiers (ie. SVMs). • Get more training images.

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