Jeffrey J. Nirschl, Andrew Janowczyk, Eliot G. Peyster, Renee Frank, Kenneth B.

Margulies, Michael D. Feldman, Anant Madabhushi,

Chapter 8 - Deep Learning Tissue Segmentation in Cardiac Histopathology Images,
Editor(s): S. Kevin Zhou, Hayit Greenspan, Dinggang Shen,
Deep Learning for Medical Image Analysis,
Academic Press,
2017,
Pages 179-195,
ISBN 9780128104088,
https://doi.org/10.1016/B978-0-12-810408-8.00011-0.
(http://www.sciencedirect.com/science/article/pii/B9780128104088000110)
Abstract: Cardiac biopsies are obtained for the diagnosis of acute heart failure as
well as post-heart-transplant rejection. On histology, both are characterized by an
expansion of the cellular and acellular stromal tissue as well as morphologic
changes within myocytes, among other features. There is growing evidence, from a
number of diseases, that computer-extracted features of tissue and nuclear
architecture are not only useful for diagnostics, but can also predict disease
recurrence, progression, and patient outcome. Automated tools to segment myocytes
and stroma with high fidelity are a critical first step toward developing
predictive models to improve diagnosis, prognosis, and reproducibility in cardiac
pathology. Whole-slide imaging in digital pathology is producing large, rich data
sets for machine learning algorithms that learn features representations directly
from data, such as deep neural networks or “deep learning”. Deep learning has
achieved state of the art performance in computer vision and is becoming ubiquitous
within the realm of digital pathology. Here, we present a deep learning framework
for myocyte and stroma segmentation in H&E stained cardiac biopsies using a data
set of 103 patients with clinical heart failure or non-heart failure controls. We
provide a tutorial for how to use the AlexNet architecture, implemented in Caffe,
to train a pixel-level classifier for segmentation. We compare the performance of
our deep learning approach to a random forest classifier with 333 intensity and
texture features and test on 20 held-out patient images with expert ground-truth
annotation of tissue boundaries. We find our deep learning segmentation outperforms
random forests in terms of mean (a) AUC (0.95 vs 0.80), (b) F-score (0.96 vs 0.91),
(c) TPR (0.96 vs 0.92), (d) TNR (0.94 vs 0.67), and (e) modified Hausdorff distance
on the segmentation perimeter pixels (51 vs 122).
Keywords: AlexNet; Caffe; Cardiology; Convolutional neural networks; Computer-aided
diagnosis (CAD); Deep learning; Digital pathology; Cardiac biopsy; Heart failure;
Hematoxylin and eosin (H&E); Whole-slide imaging (WSI)