Accurate and automatic brain metastases target delineation is a key step for efficient and effective stereotactic radiosurgery (SRS) treatment planning. In this work, we developed a deep learning convolutional neural network (CNN) algorithm for segmenting brain metastases on contrast-enhanced T1-weighted magnetic resonance imaging (MRI) datasets. We integrated the CNN-based algorithm into an automatic brain metastases segmentation workflow and validated on both Multimodal Brain Tumor Image Segmentation challenge (BRATS) data and clinical patients' data. Validation on BRATS data yielded average DICE coefficients (DCs) of 0.75±0.07 in the tumor core and 0.81±0.04 in the enhancing tumor, which outperformed most techniques in the 2015 BRATS challenge. Segmentation results of patient cases showed an average of DCs 0.67±0.03 and achieved an area under the receiver operating characteristic curve of 0.98±0.01. The developed automatic segmentation strategy surpasses current benchmark levels and offers a promising tool for SRS treatment planning for multiple brain metastases.

Compressed sensing magnetic resonance imaging (CS-MRI) is a theoretical framework that can accurately reconstruct images from undersampled k-space data with a much lower sampling rate than the one set by the classical Nyquist-Shannon sampling theorem. Therefore, CS-MRI can efficiently accelerate acquisition time and relieve the psychological burden on patients while maintaining high imaging quality. The problems with traditional CS-MRI reconstruction are solved by iterative numerical solvers, which usually suffer from expensive computational cost and the lack of accurate handcrafted priori. In this paper, inspired by deep learning’s (DL’s) fast inference and excellent end-to-end performance, we propose a novel cascaded convolutional neural network called MD-Recon-Net to facilitate fast and accurate MRI reconstruction. Especially, different from existing DL-based methods, which operate on single domain data or both domains in a certain order, our proposed MD-Recon-Net contains two parallel and interactive branches that simultaneously perform on k-space and spatial-domain data, exploring the latent relationship between k-space and the spatial domain. The simulated experimental results show that the proposed method not only achieves competitive visual effects to several state-of-the-art methods, but also outperforms other DL-based methods in terms of model scale and computational cost.

Low-dose computed tomography (LDCT) scans, which can effectively alleviate the radiation problem, will degrade the imaging quality. In this paper, we propose a novel LDCT reconstruction network that unrolls the iterative scheme and performs in both image and manifold spaces. Because patch manifolds of medical images have low-dimensional structures, we can build graphs from the manifolds. Then, we simultaneously leverage the spatial convolution to extract the local pixel-level features from the images and incorporate the graph convolution to analyze the nonlocal topological features in manifold space. The experiments show that our proposed method outperforms both the quantitative and qualitative aspects of state-of-the-art methods. In addition, aided by a projection loss component, our proposed method also demonstrates superior performance for semi-supervised learning. The network can remove most noise while maintaining the details of only 10% (40 slices) of the training data labeled.

The current mainstream computed tomography (CT) reconstruction methods based on deep learning usually need to fix the scanning geometry and dose level, which significantly aggravates the training costs and requires more training data for real clinical applications. In this paper, we propose a parameter-dependent framework (PDF) that trains a reconstruction network with data originating from multiple alternative geometries and dose levels simultaneously. In the proposed PDF, the geometry and dose level are parameterized and fed into two multilayer perceptrons (MLPs). The outputs of the MLPs are used to modulate the feature maps of the CT reconstruction network, which condition the network outputs on different geometries and dose levels. The experiments show that our proposed method can obtain competitive performance compared to the original network trained with either specific or mixed geometry and dose level, which can efficiently save extra training costs for multiple geometries and dose levels.

Due to its noninvasive character, optical coherence tomography (OCT) has become a popular diagnostic method in clinical settings. However, the low-coherence interferometric imaging procedure is inevitably contaminated by heavy speckle noise, which impairs both visual quality and diagnosis of various ocular diseases. Although deep learning has been applied for image denoising and achieved promising results, the lack of well-registered clean and noisy image pairs makes it impractical for supervised learning-based approaches to achieve satisfactory OCT image denoising results. In this paper, we propose an unsupervised OCT image speckle reduction algorithm that does not rely on well-registered image pairs. Specifically, by employing the ideas of disentangled representation and generative adversarial network, the proposed method first disentangles the noisy image into content and noise spaces by corresponding encoders. Then, the generator is used to predict the denoised OCT image with the extracted content features. In addition, the noise patches cropped from the noisy image are utilized to facilitate more accurate disentanglement. Extensive experiments have been conducted, and the results suggest that our proposed method is superior to the classic methods and demonstrates competitive performance to several recently proposed learning-based approaches in both quantitative and qualitative aspects. Code is available at: https://github.com/tsmotlp/DRGAN-OCT .

Compressed sensing (CS) computed tomography has been proven to be important for several clinical applications, such as sparse-view computed tomography (CT), digital tomosynthesis and interior tomography. Traditional compressed sensing focuses on the design of handcrafted prior regularizers, which are usually image-dependent and time-consuming. Inspired by recently proposed deep learning-based CT reconstruction models, we extend the state-of-the-art LEARN model to a dual-domain version, dubbed LEARN++. Different from existing iteration unrolling methods, which only involve projection data in the data consistency layer, the proposed LEARN++ model integrates two parallel and interactive subnetworks to perform image restoration and sinogram inpainting operations on both the image and projection domains simultaneously, which can fully explore the latent relations between projection data and reconstructed images. The experimental results demonstrate that the proposed LEARN++ model achieves competitive qualitative and quantitative results compared to several state-of-the-art methods in terms of both artifact reduction and detail preservation.