Multi-label semantic segmentation of magnetic resonance images of the prostate gland

Abstract Prostate segmentation is a substantial factor in the diagnostic pathway of suspicious prostate lesions. Medical doctors are assisted by computer-aided detection and diagnosis systems systems and methods derived from artificial intelligence deep learning-based systems have to be trained on existing data. Especially freely available labeled prostate magnetic resonance imaging data is rare. With regard to this problem, we show a method to combine two existing small datasets to form a bigger one. We present a data processing pipeline consisting of a cascaded network architecture that is able to perform multi-label semantic segmentation, hence, capable of classifying each pixel in a $$\textrm{T}_{2}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mtext>T</mml:mtext> <mml:mn>2</mml:mn> </mml:msub> </mml:math> -weighted image not only to one class but to a subset of the prostate zones and classes of interest. This delivers richer information such as overlapping zones that are key to medical radiological examination. Additionally, we describe how to integrate expert knowledge in our deep learning system. To increase data variety for training and evaluation we use image augmentation on our two datasets—a freely available dataset and our new open-source dataset. To combine the datasets we denoise the contourings in our dataset by using an effective yet simple algorithm based on standard computer vision methods only. The performance of the presented methodology is compared and evaluated using the dice score metric and 5-fold cross-validation on all datasets. Although we trained on tiny datasets our method achieves excellent segmentation quality and is even able to detect prostate cancer. Our method to combine the two datasets reduces segmentation errors and increases data variety. The proposed architecture significantly improves performance by including expert knowledge via feature-map concatenation. On the initiative for collaborative computer vision benchmarking dataset we achieve on average dice scores of approximately 91% for the whole prostate gland, 67% for the peripheral zone and 75% for the prostate central gland. We find that image augmentation except contrast limited adaptive histogram equalisation did not have much influence on the segmentation quality. Derived and enhanced from existing methods we present an approach that is able to deliver multi-label semantic segmentation results for prostate magnetic resonance imaging. This approach is simple and could be applied to other applications of deep learning as well. It improves the segmentation results by a large margin. Once tweaked to the data, our denoising and combination algorithm delivers robust and accurate results even on data with segmentation errors.