Stephen P. Pereira

Shaheer U. Saeed, João Ramalhinho, Mark Pinnock et al.

Supervised machine learning-based medical image computing applications necessitate expert label curation, while unlabelled image data might be relatively abundant. Active learning methods aim to prioritise a subset of available image data for expert annotation, for label-efficient model training. We develop a controller neural network that measures priority of images in a sequence of batches, as in batch-mode active learning, for multi-class segmentation tasks. The controller is optimised by rewarding positive task-specific performance gain, within a Markov decision process (MDP) environment that also optimises the task predictor. In this work, the task predictor is a segmentation network. A meta-reinforcement learning algorithm is proposed with multiple MDPs, such that the pre-trained controller can be adapted to a new MDP that contains data from different institutes and/or requires segmentation of different organs or structures within the abdomen. We present experimental results using multiple CT datasets from more than one thousand patients, with segmentation tasks of nine different abdominal organs, to demonstrate the efficacy of the learnt prioritisation controller function and its cross-institute and cross-organ adaptability. We show that the proposed adaptable prioritisation metric yields converging segmentation accuracy for the novel class of kidney, unseen in training, using between approximately 40\% to 60\% of labels otherwise required with other heuristic or random prioritisation metrics. For clinical datasets of limited size, the proposed adaptable prioritisation offers a performance improvement of 22.6\% and 10.2\% in Dice score, for tasks of kidney and liver vessel segmentation, respectively, compared to random prioritisation and alternative active sampling strategies.

Ester Bonmati, Yipeng Hu, Alexander Grimwood et al.

Ultrasound imaging is a commonly used technology for visualising patient anatomy in real-time during diagnostic and therapeutic procedures. High operator dependency and low reproducibility make ultrasound imaging and interpretation challenging with a steep learning curve. Automatic image classification using deep learning has the potential to overcome some of these challenges by supporting ultrasound training in novices, as well as aiding ultrasound image interpretation in patient with complex pathology for more experienced practitioners. However, the use of deep learning methods requires a large amount of data in order to provide accurate results. Labelling large ultrasound datasets is a challenging task because labels are retrospectively assigned to 2D images without the 3D spatial context available in vivo or that would be inferred while visually tracking structures between frames during the procedure. In this work, we propose a multi-modal convolutional neural network (CNN) architecture that labels endoscopic ultrasound (EUS) images from raw verbal comments provided by a clinician during the procedure. We use a CNN composed of two branches, one for voice data and another for image data, which are joined to predict image labels from the spoken names of anatomical landmarks. The network was trained using recorded verbal comments from expert operators. Our results show a prediction accuracy of 76% at image level on a dataset with 5 different labels. We conclude that the addition of spoken commentaries can increase the performance of ultrasound image classification, and eliminate the burden of manually labelling large EUS datasets necessary for deep learning applications.

Agnieszka Barbara Szczotka, Dzhoshkun Ismail Shakir, Matthew J. Clarkson et al.

Super-resolution (SR) methods have seen significant advances thanks to the development of convolutional neural networks (CNNs). CNNs have been successfully employed to improve the quality of endomicroscopy imaging. Yet, the inherent limitation of research on SR in endomicroscopy remains the lack of ground truth high-resolution (HR) images, commonly used for both supervised training and reference-based image quality assessment (IQA). Therefore, alternative methods, such as unsupervised SR are being explored. To address the need for non-reference image quality improvement, we designed a novel zero-shot super-resolution (ZSSR) approach that relies only on the endomicroscopy data to be processed in a self-supervised manner without the need for ground-truth HR images. We tailored the proposed pipeline to the idiosyncrasies of endomicroscopy by introducing both: a physically-motivated Voronoi downscaling kernel accounting for the endomicroscope's irregular fibre-based sampling pattern, and realistic noise patterns. We also took advantage of video sequences to exploit a sequence of images for self-supervised zero-shot image quality improvement. We run ablation studies to assess our contribution in regards to the downscaling kernel and noise simulation. We validate our methodology on both synthetic and original data. Synthetic experiments were assessed with reference-based IQA, while our results for original images were evaluated in a user study conducted with both expert and non-expert observers. The results demonstrated superior performance in image quality of ZSSR reconstructions in comparison to the baseline method. The ZSSR is also competitive when compared to supervised single-image SR, especially being the preferred reconstruction technique by experts.

Daniele Ravì, Agnieszka Barbara Szczotka, Stephen P Pereira et al.

In recent years, endomicroscopy has become increasingly used for diagnostic purposes and interventional guidance. It can provide intraoperative aids for real-time tissue characterization and can help to perform visual investigations aimed for example to discover epithelial cancers. Due to physical constraints on the acquisition process, endomicroscopy images, still today have a low number of informative pixels which hampers their quality. Post-processing techniques, such as Super-Resolution (SR), are a potential solution to increase the quality of these images. SR techniques are often supervised, requiring aligned pairs of low-resolution (LR) and high-resolution (HR) images patches to train a model. However, in our domain, the lack of HR images hinders the collection of such pairs and makes supervised training unsuitable. For this reason, we propose an unsupervised SR framework based on an adversarial deep neural network with a physically-inspired cycle consistency, designed to impose some acquisition properties on the super-resolved images. Our framework can exploit HR images, regardless of the domain where they are coming from, to transfer the quality of the HR images to the initial LR images. This property can be particularly useful in all situations where pairs of LR/HR are not available during the training. Our quantitative analysis, validated using a database of 238 endomicroscopy video sequences from 143 patients, shows the ability of the pipeline to produce convincing super-resolved images. A Mean Opinion Score (MOS) study also confirms this quantitative image quality assessment.