Macro-scale Neuro Segmentation
Cori Harber, Lisa Meyer-Base, Erika Moreno, Hope Mumme, Heather Whittaker
Data Analytics for Engineers: Dr. A.J. Medford and Dr. Eva Dyer
Introduction
Goal: Given a subpatch of a macroscale neuro-scan image,
we can classify the subpatch by brain area.
Classes:
Dataset: 92,160 total images, 128x128 are parent images
taken from patch, 64x64 images are rotated within the
subpatches
Approach
Baseline: A logistic regression model was trained using
mean, variance, and sum of the entropy filter on the
128x128 images. Training accuracy was 73.9% and testing
accuracy was 74.7%
Methods
Feature Extraction
● Feature Set 1: Entropy Mean-Variance-Sum, Shape Intensity M-V-S, Pixel
Intensity M-V-S, Histogram of Oriented Gradients (HOG) M-V-S
● Feature Set 2: Feature Set 1, and Average Alpha Class 0-1-2, Sum Alpha
Class 0-1-2, L2 Norm Alpha Class 0-1-2, L2 Norm Accuracy Class 0-1-2
Dimensionality Reduction
3D Projection of Feature Set #1
Classification
● Train/Test split - 70 train, 30 test
● k-Nearest Neighbors, kernel SVM, Decision Tree, linear SVM,
logistic regression.
● The underlying distribution of the data is unknown, and the data is
nearly linearly separable. Therefore, non-linear non-parametric
classifiers such as kNN, KSVM, DT are expected to do better than
linear parametric classifiers such as Linear SVM and LR.
Kernel SVM Formula
Results
Feature Set #1 Feature Set #2
Test Accuracy for Feature Set #1
● The highest average testing accuracy was achieved prior to
dimensionality reduction at 97.6%.
● scaled PCA of the top 5 features came in first place with an average
accuracy across all classifiers of 85.21%.
● Kernel SVM using the rbf kernel did the best.
○ The best performing classifier in all five cases, achieving 97% test-set
accuracy.
● Performance for linear classifiers logistic regression and linear SVM
improved using feature set #2.
Feature Set #1 Feature Set #2
Conclusion
● Achieved 97% testing accuracy, with Kernel SVM and kNN
producing the best results, either without dimensionality
reduction or using scaled PCA with 5 components.
● The success of this work could potentially aid in automated
neuro-image segmentation for large-scale neuro-images
○ alleviating manual annotation workloads for humans
○ speeding analytical pipelines.