We present an automated approach for rating HER2 over-expressions in given whole-slide images of breast cancer histology slides. The slides have a very high resolution and only a small part of it is relevant for the rating.
Our approach is based on Convolutional Neural Networks (CNN), which are directly modelling the whole computer vision pipeline, from feature extraction to classification, with a single parameterized model. CNN models have led to a significant breakthrough in a lot of vision applications and showed promising results for medical tasks. However, the required size of training data is still an issue. Our CNN models are pre-trained on a large set of datasets of non-medical images, which prevents over-fitting to the small annotated dataset available in our case. We assume the selection of the probe in the data with just a single mouse click defining a point of interest. This is reasonable especially for slices acquired together with another sample. We sample image patches around the point of interest and obtain bilinear features by passing them through a CNN and encoding the output of the last convolutional layer with its second-order statistics.
Our approach ranked second in the Her2 contest held by the University of Warwick achieving 345 points compared to 348 points of the winning team. In addition to pure classification, our approach would also allow for localization of parts of the slice relevant for visual detection of Her2 over-expression.