Christoph Baur

AggNet: Deep Learning From Crowds for Mitosis Detection in Breast Cancer Histology Images

The lack of publicly available ground-truth data has been identified as the major challenge for transferring recent developments in deep learning to the biomedical imaging domain. Though crowdsourcing has enabled annotation of large scale databases for real world images, its application for biomedical purposes requires a deeper understanding and hence, more precise definition of the actual annotation task. The fact that expert tasks are being outsourced to non-expert users may lead to noisy annotations introducing disagreement between users. Despite being a valuable resource for learning annotation models from crowdsourcing, conventional machine-learning methods may have difficulties dealing with noisy annotations during training. In this manuscript, we present a new concept for learning from crowds that handle data aggregation directly as part of the learning process of the convolutional neural network (CNN) via additional crowdsourcing layer (AggNet). Besides, we present an experimental study on learning from crowds designed to answer the following questions. 1) Can deep CNN be trained with data collected from crowdsourcing? 2) How to adapt the CNN to train on multiple types of annotation datasets (ground truth and crowd-based)? 3) How does the choice of annotation and aggregation affect the accuracy? Our experimental setup involved Annot8, a self-implemented web-platform based on Crowdflower API realizing image annotation tasks for a publicly available biomedical image database. Our results give valuable insights into the functionality of deep CNN learning from crowd annotations and prove the necessity of data aggregation integration.The lack of publicly available ground-truth data has been identified as the major challenge for transferring recent developments in deep learning to the biomedical imaging domain. Though crowdsourcing has enabled annotation of large scale databases for real world images, its application for biomedical purposes requires a deeper understanding and hence, more precise definition of the actual annotation task. The fact that expert tasks are being outsourced to non-expert users may lead to noisy annotations introducing disagreement between users. Despite being a valuable resource for learning annotation models from crowdsourcing, conventional machine-learning methods may have difficulties dealing with noisy annotations during training. In this manuscript, we present a new concept for learning from crowds that handle data aggregation directly as part of the learning process of the convolutional neural network (CNN) via additional crowdsourcing layer (AggNet). Besides, we present an experimental study on learning from crowds designed to answer the following questions. 1) Can deep CNN be trained with data collected from crowdsourcing? 2) How to adapt the CNN to train on multiple types of annotation datasets (ground truth and crowd-based)? 3) How does the choice of annotation and aggregation affect the accuracy? Our experimental setup involved Annot8, a self-implemented web-platform based on Crowdflower API realizing image annotation tasks for a publicly available biomedical image database. Our results give valuable insights into the functionality of deep CNN learning from crowd annotations and prove the necessity of data aggregation integration.

Semi-supervised Deep Learning for Fully Convolutional Networks

Deep learning usually requires large amounts of labeled training data, but annotating data is costly and tedious. The framework of semi-supervised learning provides the means to use both labeled data and arbitrary amounts of unlabeled data for training. Recently, semi-supervised deep learning has been intensively studied for standard CNN architectures. However, Fully Convolutional Networks (FCNs) set the state-of-the-art for many image segmentation tasks. To the best of our knowledge, there is no existing semi-supervised learning method for such FCNs yet. We lift the concept of auxiliary manifold embedding for semi-supervised learning to FCNs with the help of Random Feature Embedding. In our experiments on the challenging task of MS Lesion Segmentation, we leverage the proposed framework for the purpose of domain adaptation and report substantial improvements over the baseline model.

CathNets: Detection and Single-View Depth Prediction of Catheter Electrodes

The recent success of convolutional neural networks in many computer vision tasks implies that their application could also be beneficial for vision tasks in cardiac electrophysiology procedures which are commonly carried out under guidance of C-arm fluoroscopy. Many efforts for catheter detection and reconstruction have been made, but especially robust detection of catheters in X-ray images in realtime is still not entirely solved. We propose two novel methods for (i) fully automatic electrophysiology catheter electrode detection in interventional X-ray images and (ii) single-view depth estimation of such electrodes based on convolutional neural networks. For (i), experiments on 24 different fluoroscopy sequences (1650 X-ray images) yielded a detection rate > 99 %. Our experiments on (ii) depth prediction using 20 images with depth information available revealed that we are able to estimate the depth of catheter tips in the lateral view with a remarkable mean error of \(6.08\,\pm \,4.66\) mm.

Generating Highly Realistic Images of Skin Lesions with GANs

As many other machine learning driven medical image analysis tasks, skin image analysis suffers from a chronic lack of labeled data and skewed class distributions, which poses problems for the training of robust and well-generalizing models. The ability to synthesize realistic looking images of skin lesions could act as a reliever for the aforementioned problems. Generative Adversarial Networks (GANs) have been successfully used to synthesize realistically looking medical images, however limited to low resolution, whereas machine learning models for challenging tasks such as skin lesion segmentation or classification benefit from much higher resolution data. In this work, we successfully synthesize realistically looking images of skin lesions with GANs at such high resolution. Therefore, we utilize the concept of progressive growing, which we both quantitatively and qualitatively compare to other GAN architectures such as the DCGAN and the LAPGAN. Our results show that with the help of progressive growing, we can synthesize highly realistic dermoscopic images of skin lesions that even expert dermatologists find hard to distinguish from real ones.

Robust navigation support in lowest dose image setting

PurposeClinical cardiac electrophysiology (EP) is concerned with diagnosis and treatment of cardiac arrhythmia describing abnormality or perturbation in the normal activation sequence of the myocardium. With the recent introduction of lowest dose X-ray imaging protocol for EP procedures, interventional image enhancement has gained crucial importance for the well-being of patients as well as medical staff.MethodsIn this paper, we introduce a novel method to detect and track different EP catheter electrodes in lowest dose fluoroscopic sequences based on

StainGAN: Stain Style Transfer for Digital Histological Images.

\ell _1

Deep Autoencoding Models for Unsupervised Anomaly Segmentation in Brain MR Images.

ℓ1-sparse coding and online robust PCA (ORPCA). Besides being able to work on real lowest dose sequences, the underlying methodology achieves simultaneous detection and tracking of three main EP catheters used during ablation procedures.ResultsWe have validated our algorithm on 16 lowest dose fluoroscopic sequences acquired during real cardiac ablation procedures. In addition to expert labels for 2 sequences, we have employed a crowdsourcing strategy to obtain ground truth labels for the remaining 14 sequences. In order to validate the effect of different training data, we have employed a leave-one-out cross-validation scheme yielding an average detection rate of