Real-time standard scan plane detection and localisation in fetal ultrasound using fully convolutional neural networks

Fetal mid-pregnancy scans are typically carried out according to fixed protocols. Accurate detection of abnormalities and correct biometric measurements hinge on the correct acquisition of clearly defined standard scan planes. Locating these standard planes requires a high level of expertise. However, there is a worldwide shortage of expert sonographers. In this paper, we consider a fully automated system based on convolutional neural networks which can detect twelve standard scan planes as defined by the UK fetal abnormality screening programme. The network design allows real-time inference and can be naturally extended to provide an approximate localisation of the fetal anatomy in the image. Such a framework can be used to automate or assist with scan plane selection, or for the retrospective retrieval of scan planes from recorded videos. The method is evaluated on a large database of 1003 volunteer mid-pregnancy scans. We show that standard planes acquired in a clinical scenario are robustly detected with a precision and recall of 69 % and 80 %, which is superior to the current state-of-the-art. Furthermore, we show that it can retrospectively retrieve correct scan planes with an accuracy of 71 % for cardiac views and 81 % for non-cardiac views

SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound

Identifying and interpreting fetal standard scan planes during 2D ultrasound mid-pregnancy examinations are highly complex tasks which require years of training. Apart from guiding the probe to the correct location, it can be equally difficult for a non-expert to identify relevant structures within the image. Automatic image processing can provide tools to help experienced as well as inexperienced operators with these tasks. In this paper, we propose a novel method based on convolutional neural networks which can automatically detect 13 fetal standard views in freehand 2D ultrasound data as well as provide a localisation of the fetal structures via a bounding box. An important contribution is that the network learns to localise the target anatomy using weak supervision based on image-level labels only. The network architecture is designed to operate in real-time while providing optimal output for the localisation task. We present results for real-time annotation, retrospective frame retrieval from saved videos, and localisation on a very large and challenging dataset consisting of images and video recordings of full clinical anomaly screenings. We found that the proposed method achieved an average F1-score of 0.798 in a realistic classification experiment modelling real-time detection, and obtained a 90.09% accuracy for retrospective frame retrieval. Moreover, an accuracy of 77.8% was achieved on the localisation task.Comment: 12 pages, 8 figures, published in IEEE Transactions in Medical Imagin

Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images

We propose a novel attention gate (AG) model for medical image analysis that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules when using convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed AG models are evaluated on a variety of tasks, including medical image classification and segmentation. For classification, we demonstrate the use case of AGs in scan plane detection for fetal ultrasound screening. We show that the proposed attention mechanism can provide efficient object localisation while improving the overall prediction performance by reducing false positives. For segmentation, the proposed architecture is evaluated on two large 3D CT abdominal datasets with manual annotations for multiple organs. Experimental results show that AG models consistently improve the prediction performance of the base architectures across different datasets and training sizes while preserving computational efficiency. Moreover, AGs guide the model activations to be focused around salient regions, which provides better insights into how model predictions are made. The source code for the proposed AG models is publicly available.Comment: Accepted for Medical Image Analysis (Special Issue on Medical Imaging with Deep Learning). arXiv admin note: substantial text overlap with arXiv:1804.03999, arXiv:1804.0533

Temporal HeartNet: Towards Human-Level Automatic Analysis of Fetal Cardiac Screening Video

We present an automatic method to describe clinically useful information about scanning, and to guide image interpretation in ultrasound (US) videos of the fetal heart. Our method is able to jointly predict the visibility, viewing plane, location and orientation of the fetal heart at the frame level. The contributions of the paper are three-fold: (i) a convolutional neural network architecture is developed for a multi-task prediction, which is computed by sliding a 3x3 window spatially through convolutional maps. (ii) an anchor mechanism and Intersection over Union (IoU) loss are applied for improving localization accuracy. (iii) a recurrent architecture is designed to recursively compute regional convolutional features temporally over sequential frames, allowing each prediction to be conditioned on the whole video. This results in a spatial-temporal model that precisely describes detailed heart parameters in challenging US videos. We report results on a real-world clinical dataset, where our method achieves performance on par with expert annotations.Comment: To appear in MICCAI, 201

Deep Learning using K-space Based Data Augmentation for Automated Cardiac MR Motion Artefact Detection

Quality assessment of medical images is essential for complete automation of image processing pipelines. For large population studies such as the UK Biobank, artefacts such as those caused by heart motion are problematic and manual identification is tedious and time-consuming. Therefore, there is an urgent need for automatic image quality assessment techniques. In this paper, we propose a method to automatically detect the presence of motion-related artefacts in cardiac magnetic resonance (CMR) images. As this is a highly imbalanced classification problem (due to the high number of good quality images compared to the low number of images with motion artefacts), we propose a novel k-space based training data augmentation approach in order to address this problem. Our method is based on 3D spatio-temporal Convolutional Neural Networks, and is able to detect 2D+time short axis images with motion artefacts in less than 1ms. We test our algorithm on a subset of the UK Biobank dataset consisting of 3465 CMR images and achieve not only high accuracy in detection of motion artefacts, but also high precision and recall. We compare our approach to a range of state-of-the-art quality assessment methods.Comment: Accepted for MICCAI2018 Conferenc

FetalNet: Multi-task Deep Learning Framework for Fetal Ultrasound Biometric Measurements

In this paper, we propose an end-to-end multi-task neural network called FetalNet with an attention mechanism and stacked module for spatio-temporal fetal ultrasound scan video analysis. Fetal biometric measurement is a standard examination during pregnancy used for the fetus growth monitoring and estimation of gestational age and fetal weight. The main goal in fetal ultrasound scan video analysis is to find proper standard planes to measure the fetal head, abdomen and femur. Due to natural high speckle noise and shadows in ultrasound data, medical expertise and sonographic experience are required to find the appropriate acquisition plane and perform accurate measurements of the fetus. In addition, existing computer-aided methods for fetal US biometric measurement address only one single image frame without considering temporal features. To address these shortcomings, we propose an end-to-end multi-task neural network for spatio-temporal ultrasound scan video analysis to simultaneously localize, classify and measure the fetal body parts. We propose a new encoder-decoder segmentation architecture that incorporates a classification branch. Additionally, we employ an attention mechanism with a stacked module to learn salient maps to suppress irrelevant US regions and efficient scan plane localization. We trained on the fetal ultrasound video comes from routine examinations of 700 different patients. Our method called FetalNet outperforms existing state-of-the-art methods in both classification and segmentation in fetal ultrasound video recordings.Comment: Accepted to 28th International Conference on Neural Information Processing (ICONIP) 2021, Bali, Indonesia, 8-12 December, 202

Deep learning for fast and robust medical image reconstruction and analysis

Medical imaging is an indispensable component of modern medical research as well as clinical practice. Nevertheless, imaging techniques such as magnetic resonance imaging (MRI) and computational tomography (CT) are costly and are less accessible to the majority of the world. To make medical devices more accessible, affordable and efficient, it is crucial to re-calibrate our current imaging paradigm for smarter imaging. In particular, as medical imaging techniques have highly structured forms in the way they acquire data, they provide us with an opportunity to optimise the imaging techniques holistically by leveraging data. The central theme of this thesis is to explore different opportunities where we can exploit data and deep learning to improve the way we extract information for better, faster and smarter imaging. This thesis explores three distinct problems. The first problem is the time-consuming nature of dynamic MR data acquisition and reconstruction. We propose deep learning methods for accelerated dynamic MR image reconstruction, resulting in up to 10-fold reduction in imaging time. The second problem is the redundancy in our current imaging pipeline. Traditionally, imaging pipeline treated acquisition, reconstruction and analysis as separate steps. However, we argue that one can approach them holistically and optimise the entire pipeline jointly for a specific target goal. To this end, we propose deep learning approaches for obtaining high fidelity cardiac MR segmentation directly from significantly undersampled data, greatly exceeding the undersampling limit for image reconstruction. The final part of this thesis tackles the problem of interpretability of the deep learning algorithms. We propose attention-models that can implicitly focus on salient regions in an image to improve accuracy for ultrasound scan plane detection and CT segmentation. More crucially, these models can provide explainability, which is a crucial stepping stone for the harmonisation of smart imaging and current clinical practice.Open Acces

Improving Fetal Head Contour Detection by Object Localisation with Deep Learning

Ultrasound-based fetal head biometrics measurement is a key indicator in monitoring the conditions of fetuses. Since manual measurement of relevant anatomical structures of fetal head is time-consuming and subject to inter-observer variability, there has been strong interest in finding automated, robust, accurate and reliable method. In this paper, we propose a deep learning-based method to segment fetal head from ultrasound images. The proposed method formulates the detection of fetal head boundary as a combined object localisation and segmentation problem based on deep learning model. Incorporating an object localisation in a framework developed for segmentation purpose aims to improve the segmentation accuracy achieved by fully convolutional network. Finally, ellipse is fitted on the contour of the segmented fetal head using least-squares ellipse fitting method. The proposed model is trained on 999 2-dimensional ultrasound images and tested on 335 images achieving Dice coefficient of$$97.73 \pm 1.32$$. The experimental results demonstrate that the proposed deep learning method is promising in automatic fetal head detection and segmentation

Recent Advances in Artificial Intelligence-Assisted Ultrasound Scanning

Funded by the Spanish Ministry of Economic Affairs and Digital Transformation (Project MIA.2021.M02.0005 TARTAGLIA, from the Recovery, Resilience, and Transformation Plan financed by the European Union through Next Generation EU funds). TARTAGLIA takes place under the R&D Missions in Artificial Intelligence program, which is part of the Spain Digital 2025 Agenda and the Spanish National Artificial Intelligence Strategy.Ultrasound (US) is a flexible imaging modality used globally as a first-line medical exam procedure in many different clinical cases. It benefits from the continued evolution of ultrasonic technologies and a well-established US-based digital health system. Nevertheless, its diagnostic performance still presents challenges due to the inherent characteristics of US imaging, such as manual operation and significant operator dependence. Artificial intelligence (AI) has proven to recognize complicated scan patterns and provide quantitative assessments for imaging data. Therefore, AI technology has the potential to help physicians get more accurate and repeatable outcomes in the US. In this article, we review the recent advances in AI-assisted US scanning. We have identified the main areas where AI is being used to facilitate US scanning, such as standard plane recognition and organ identification, the extraction of standard clinical planes from 3D US volumes, and the scanning guidance of US acquisitions performed by humans or robots. In general, the lack of standardization and reference datasets in this field makes it difficult to perform comparative studies among the different proposed methods. More open-access repositories of large US datasets with detailed information about the acquisition are needed to facilitate the development of this very active research field, which is expected to have a very positive impact on US imaging.Depto. de Estructura de la Materia, Física Térmica y ElectrónicaFac. de Ciencias FísicasTRUEMinistry of Economic Affairs and Digital Transformation from the Recovery, Resilience, and Transformation PlanNext Generation EU fundspu