DOI

10.17077/etd.jgiv-7i2q

Document Type

Dissertation

Date of Degree

Fall 2018

Degree Name

PhD (Doctor of Philosophy)

Degree In

Biomedical Engineering

First Advisor

Reinhardt, Joseph M.

First Committee Member

Hoffman, Eric A.

Second Committee Member

Christensen, Gary E.

Third Committee Member

Bayouth, John E.

Fourth Committee Member

Johnson, Hans J.

Abstract

Computed tomography (CT) is routinely used for diagnosing lung disease and developing treatment plans using images of intricate lung structure with submillimeter resolution. Automated segmentation of anatomical structures in such images is important to enable efficient processing in clinical and research settings. Convolution neural networks (ConvNets) are largely successful at performing image segmentation with the ability to learn discriminative abstract features that yield generalizable predictions. However, constraints in hardware memory do not allow deep networks to be trained with high-resolution volumetric CT images. Restricted by memory constraints, current applications of ConvNets on volumetric medical images use a subset of the full image; limiting the capacity of the network to learn informative global patterns. Local patterns, such as edges, are necessary for precise boundary localization, however, they suffer from low specificity. Global information can disambiguate structures that are locally similar.

The central thesis of this doctoral work is that both local and global information is important for segmentation of anatomical structures in medical images. A novel multi-scale ConvNet is proposed that divides the learning task across multiple networks; each network learns features over different ranges of scales. It is hypothesized that multi-scale ConvNets will lead to improved segmentation performance, as no compromise needs to be made between image resolution, image extent, and network depth. Three multi-scale models were designed to specifically target segmentation of three pulmonary structures: lungs, fissures, and lobes.

The proposed models were evaluated on a diverse datasets and compared to architectures that do not use both local and global features. The lung model was evaluated on humans and three animal species; the results demonstrated the multi-scale model outperformed single scale models at different resolutions. The fissure model showed superior performance compared to both a traditional Hessian filter and a standard U-Net architecture that is limited in global extent.

The results demonstrated that multi-scale ConvNets improved pulmonary CT segmentation by incorporating both local and global features using multiple ConvNets within a constrained-memory system. Overall, the proposed pipeline achieved high accuracy and was robust to variations resulting from different imaging protocols, reconstruction kernels, scanners, lung volumes, and pathological alterations; demonstrating its potential for enabling high-throughput image analysis in clinical and research settings.

Keywords

Computed Tomography, Convolutional Neural Networks, Deep Learning, Pulmonary, Segmentation

Pages

xvi, 175 pages

Bibliography

Includes bibliographical references (pages 158-175).

Comments

This thesis has been optimized for improved web viewing. If you require the original version, contact the University Archives at the University of Iowa: http://www.lib.uiowa.edu/sc/contact/

Copyright

Copyright © 2018 Sarah E. Gerard

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