NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

Constrained CycleGAN for Effective Generation of Ultrasound Sector Images of Improved Spatial Resolution

Objective. A phased or a curvilinear array produces ultrasound (US) images with a sector field of view (FOV), which inherently exhibits spatially-varying image resolution with inferior quality in the far zone and towards the two sides azimuthally. Sector US images with improved spatial resolutions are favorable for accurate quantitative analysis of large and dynamic organs, such as the heart. Therefore, this study aims to translate US images with spatially-varying resolution to ones with less spatially-varying resolution. CycleGAN has been a prominent choice for unpaired medical image translation; however, it neither guarantees structural consistency nor preserves backscattering patterns between input and generated images for unpaired US images. Approach. To circumvent this limitation, we propose a constrained CycleGAN (CCycleGAN), which directly performs US image generation with unpaired images acquired by different ultrasound array probes. In addition to conventional adversarial and cycle-consistency losses of CycleGAN, CCycleGAN introduces an identical loss and a correlation coefficient loss based on intrinsic US backscattered signal properties to constrain structural consistency and backscattering patterns, respectively. Instead of post-processed B-mode images, CCycleGAN uses envelope data directly obtained from beamformed radio-frequency signals without any other non-linear postprocessing. Main Results. In vitro phantom results demonstrate that CCycleGAN successfully generates images with improved spatial resolution as well as higher peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) compared with benchmarks. Significance. CCycleGAN-generated US images of the in vivo human beating heart further facilitate higher quality heart wall motion estimation than benchmarks-generated ones, particularly in deep regions

Incorporating Ultrasound Tongue Images for Audio-Visual Speech Enhancement

Audio-visual speech enhancement (AV-SE) aims to enhance degraded speech along with extra visual information such as lip videos, and has been shown to be more effective than audio-only speech enhancement. This paper proposes the incorporation of ultrasound tongue images to improve the performance of lip-based AV-SE systems further. To address the challenge of acquiring ultrasound tongue images during inference, we first propose to employ knowledge distillation during training to investigate the feasibility of leveraging tongue-related information without directly inputting ultrasound tongue images. Specifically, we guide an audio-lip speech enhancement student model to learn from a pre-trained audio-lip-tongue speech enhancement teacher model, thus transferring tongue-related knowledge. To better model the alignment between the lip and tongue modalities, we further propose the introduction of a lip-tongue key-value memory network into the AV-SE model. This network enables the retrieval of tongue features based on readily available lip features, thereby assisting the subsequent speech enhancement task. Experimental results demonstrate that both methods significantly improve the quality and intelligibility of the enhanced speech compared to traditional lip-based AV-SE baselines. Moreover, both proposed methods exhibit strong generalization performance on unseen speakers and in the presence of unseen noises. Furthermore, phone error rate (PER) analysis of automatic speech recognition (ASR) reveals that while all phonemes benefit from introducing ultrasound tongue images, palatal and velar consonants benefit most.Comment: Submmited to IEEE/ACM Transactions on Audio, Speech and Language Processing. arXiv admin note: text overlap with arXiv:2305.1493

Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions

Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in the deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. In this paper, we provide an extensive survey of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods, publicly available datasets, and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are described in detail. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.Comment: Survey, 41 page

Comparative Analysis of Segment Anything Model and U-Net for Breast Tumor Detection in Ultrasound and Mammography Images

In this study, the main objective is to develop an algorithm capable of identifying and delineating tumor regions in breast ultrasound (BUS) and mammographic images. The technique employs two advanced deep learning architectures, namely U-Net and pretrained SAM, for tumor segmentation. The U-Net model is specifically designed for medical image segmentation and leverages its deep convolutional neural network framework to extract meaningful features from input images. On the other hand, the pretrained SAM architecture incorporates a mechanism to capture spatial dependencies and generate segmentation results. Evaluation is conducted on a diverse dataset containing annotated tumor regions in BUS and mammographic images, covering both benign and malignant tumors. This dataset enables a comprehensive assessment of the algorithm's performance across different tumor types. Results demonstrate that the U-Net model outperforms the pretrained SAM architecture in accurately identifying and segmenting tumor regions in both BUS and mammographic images. The U-Net exhibits superior performance in challenging cases involving irregular shapes, indistinct boundaries, and high tumor heterogeneity. In contrast, the pretrained SAM architecture exhibits limitations in accurately identifying tumor areas, particularly for malignant tumors and objects with weak boundaries or complex shapes. These findings highlight the importance of selecting appropriate deep learning architectures tailored for medical image segmentation. The U-Net model showcases its potential as a robust and accurate tool for tumor detection, while the pretrained SAM architecture suggests the need for further improvements to enhance segmentation performance