Long-term Dependency for 3D Reconstruction of Freehand Ultrasound Without External Tracker

Objective: Reconstructing freehand ultrasound in 3D without any external tracker has been a long-standing challenge in ultrasound-assisted procedures. We aim to define new ways of parameterising long-term dependencies, and evaluate the performance. Methods: First, long-term dependency is encoded by transformation positions within a frame sequence. This is achieved by combining a sequence model with a multi-transformation prediction. Second, two dependency factors are proposed, anatomical image content and scanning protocol, for contributing towards accurate reconstruction. Each factor is quantified experimentally by reducing respective training variances. Results: 1) The added long-term dependency up to 400 frames at 20 frames per second (fps) indeed improved reconstruction, with an up to 82.4% lowered accumulated error, compared with the baseline performance. The improvement was found to be dependent on sequence length, transformation interval and scanning protocol and, unexpectedly, not on the use of recurrent networks with long-short term modules; 2) Decreasing either anatomical or protocol variance in training led to poorer reconstruction accuracy. Interestingly, greater performance was gained from representative protocol patterns, than from representative anatomical features. Conclusion: The proposed algorithm uses hyperparameter tuning to effectively utilise long-term dependency. The proposed dependency factors are of practical significance in collecting diverse training data, regulating scanning protocols and developing efficient networks. Significance: The proposed new methodology with publicly available volunteer data and code for parametersing the long-term dependency, experimentally shown to be valid sources of performance improvement, which could potentially lead to better model development and practical optimisation of the reconstruction application.

Privileged Anatomical and Protocol Discrimination in Trackerless 3D Ultrasound Reconstruction

Three-dimensional (3D) freehand ultrasound (US) reconstruction without using any additional external tracking device has seen recent advances with deep neural networks (DNNs). In this paper, we first investigated two identified contributing factors of the learned inter-frame correlation that enable the DNN-based reconstruction: anatomy and protocol. We propose to incorporate the ability to represent these two factors - readily available during training - as the privileged information to improve existing DNN-based methods. This is implemented in a new multi-task method, where the anatomical and protocol discrimination are used as auxiliary tasks. We further develop a differentiable network architecture to optimise the branching location of these auxiliary tasks, which controls the ratio between shared and task-specific network parameters, for maximising the benefits from the two auxiliary tasks. Experimental results, on a dataset with 38 forearms of 19 volunteers acquired with 6 different scanning protocols, show that 1) both anatomical and protocol variances are enabling factors for DNN-based US reconstruction; 2) learning how to discriminate different subjects (anatomical variance) and predefined types of scanning paths (protocol variance) both significantly improve frame prediction accuracy, volume reconstruction overlap, accumulated tracking error and final drift, using the proposed algorithm.

Combiner and HyperCombiner Networks: Rules to Combine Multimodality MR Images for Prostate Cancer Localisation

One of the distinct characteristics in radiologists' reading of multiparametric prostate MR scans, using reporting systems such as PI-RADS v2.1, is to score individual types of MR modalities, T2-weighted, diffusion-weighted, and dynamic contrast-enhanced, and then combine these image-modality-specific scores using standardised decision rules to predict the likelihood of clinically significant cancer. This work aims to demonstrate that it is feasible for low-dimensional parametric models to model such decision rules in the proposed Combiner networks, without compromising the accuracy of predicting radiologic labels: First, it is shown that either a linear mixture model or a nonlinear stacking model is sufficient to model PI-RADS decision rules for localising prostate cancer. Second, parameters of these (generalised) linear models are proposed as hyperparameters, to weigh multiple networks that independently represent individual image modalities in the Combiner network training, as opposed to end-to-end modality ensemble. A HyperCombiner network is developed to train a single image segmentation network that can be conditioned on these hyperparameters during inference, for much improved efficiency. Experimental results based on data from 850 patients, for the application of automating radiologist labelling multi-parametric MR, compare the proposed combiner networks with other commonly-adopted end-to-end networks. Using the added advantages of obtaining and interpreting the modality combining rules, in terms of the linear weights or odds-ratios on individual image modalities, three clinical applications are presented for prostate cancer segmentation, including modality availability assessment, importance quantification and rule discovery.

Active learning using adaptable task-based prioritisation

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.

Trackerless freehand ultrasound with sequence modelling and auxiliary transformation over past and future frames

Three-dimensional (3D) freehand ultrasound (US) reconstruction without a tracker can be advantageous over its two-dimensional or tracked counterparts in many clinical applications. In this paper, we propose to estimate 3D spatial transformation between US frames from both past and future 2D images, using feed-forward and recurrent neural networks (RNNs). With the temporally available frames, a further multi-task learning algorithm is proposed to utilise a large number of auxiliary transformation-predicting tasks between them. Using more than 40,000 US frames acquired from 228 scans on 38 forearms of 19 volunteers in a volunteer study, the hold-out test performance is quantified by frame prediction accuracy, volume reconstruction overlap, accumulated tracking error and final drift, based on ground-truth from an optical tracker. The results show the importance of modelling the temporal-spatially correlated input frames as well as output transformations, with further improvement owing to additional past and/or future frames. The best performing model was associated with predicting transformation between moderately-spaced frames, with an interval of less than ten frames at 20 frames per second (fps). Little benefit was observed by adding frames more than one second away from the predicted transformation, with or without LSTM-based RNNs. Interestingly, with the proposed approach, explicit within-sequence loss that encourages consistency in composing transformations or minimises accumulated error may no longer be required. The implementation code and volunteer data will be made publicly available ensuring reproducibility and further research.

Collaborative Quantization Embeddings for Intra-Subject Prostate MR Image Registration

Image registration is useful for quantifying morphological changes in longitudinal MR images from prostate cancer patients. This paper describes a development in improving the learning-based registration algorithms, for this challenging clinical application often with highly variable yet limited training data. First, we report that the latent space can be clustered into a much lower dimensional space than that commonly found as bottleneck features at the deep layer of a trained registration network. Based on this observation, we propose a hierarchical quantization method, discretizing the learned feature vectors using a jointly-trained dictionary with a constrained size, in order to improve the generalisation of the registration networks. Furthermore, a novel collaborative dictionary is independently optimised to incorporate additional prior information, such as the segmentation of the gland or other regions of interest, in the latent quantized space. Based on 216 real clinical images from 86 prostate cancer patients, we show the efficacy of both the designed components. Improved registration accuracy was obtained with statistical significance, in terms of both Dice on gland and target registration error on corresponding landmarks, the latter of which achieved 5.46 mm, an improvement of 28.7\% from the baseline without quantization. Experimental results also show that the difference in performance was indeed minimised between training and testing data.

You Never Cluster Alone

Recent advances in self-supervised learning with instance-level contrastive objectives facilitate unsupervised clustering. However, a standalone datum is not perceiving the context of the holistic cluster, and may undergo sub-optimal assignment. In this paper, we extend the mainstream contrastive learning paradigm to a cluster-level scheme, where all the data subjected to the same cluster contribute to a unified representation that encodes the context of each data group. Contrastive learning with this representation then rewards the assignment of each datum. To implement this vision, we propose twin-contrast clustering (TCC). We define a set of categorical variables as clustering assignment confidence, which links the instance-level learning track with the cluster-level one. On one hand, with the corresponding assignment variables being the weight, a weighted aggregation along the data points implements the set representation of a cluster. We further propose heuristic cluster augmentation equivalents to enable cluster-level contrastive learning. On the other hand, we derive the evidence lower-bound of the instance-level contrastive objective with the assignments. By reparametrizing the assignment variables, TCC is trained end-to-end, requiring no alternating steps. Extensive experiments show that TCC outperforms the state-of-the-art on challenging benchmarks.

Understanding and Correcting Low-quality Retinal Fundus Images for Clinical Analysis

Retinal fundus images are widely used for clinical screening and diagnosis of eye diseases. However, fundus images captured by operators with various levels of experiences have a large variation in quality. Low-quality fundus images increase the uncertainty in clinical observation and lead to a risk of misdiagnosis. Due to the special optical beam of fundus imaging and retinal structure, the natural image enhancement methods cannot be utilized directly. In this paper, we first analyze the ophthalmoscope imaging system and model the reliable degradation of major inferior-quality factors, including uneven illumination, blur, and artifacts. Then, based on the degradation model, a clinical-oriented fundus enhancement network~(cofe-Net)~is proposed to suppress the global degradation factors, and simultaneously preserve anatomical retinal structures and pathological characteristics for clinical observation and analysis. Experiments on both synthetic and real fundus images demonstrate that our algorithm effectively corrects low-quality fundus images without losing retinal details. Moreover, we also show that the fundus correction method can benefit medical image analysis applications, e.g, retinal vessel segmentation and optic disc/cup detection.

Deep Semantic Face Deblurring

In this paper, we propose an effective and efficient face deblurring algorithm by exploiting semantic cues via deep convolutional neural networks. As the human faces are highly structured and share unified facial components (e.g., eyes and mouths), such semantic information provides a strong prior for restoration. We incorporate face semantic labels as input priors and propose an adaptive structural loss to regularize facial local structures within an end-to-end deep convolutional neural network. Specifically, we first use a coarse deblurring network to reduce the motion blur on the input face image. We then adopt a parsing network to extract the semantic features from the coarse deblurred image. Finally, the fine deblurring network utilizes the semantic information to restore a clear face image. We train the network with perceptual and adversarial losses to generate photo-realistic results. The proposed method restores sharp images with more accurate facial features and details. Quantitative and qualitative evaluations demonstrate that the proposed face deblurring algorithm performs favorably against the state-of-the-art methods in terms of restoration quality, face recognition and execution speed.

Human-Aware Motion Deblurring

This paper proposes a human-aware deblurring model that disentangles the motion blur between foreground (FG) humans and background (BG). The proposed model is based on a triple-branch encoder-decoder architecture. The first two branches are learned for sharpening FG humans and BG details, respectively; while the third one produces global, harmonious results by comprehensively fusing multi-scale deblurring information from the two domains. The proposed model is further endowed with a supervised, human-aware attention mechanism in an end-to-end fashion. It learns a soft mask that encodes FG human information and explicitly drives the FG/BG decoder-branches to focus on their specific domains. To further benefit the research towards Human-aware Image Deblurring, we introduce a large-scale dataset, named HIDE, which consists of 8,422 blurry and sharp image pairs with 65,784 densely annotated FG human bounding boxes. HIDE is specifically built to span a broad range of scenes, human object sizes, motion patterns, and background complexities. Extensive experiments on public benchmarks and our dataset demonstrate that our model performs favorably against the state-of-the-art motion deblurring methods, especially in capturing semantic details.