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Register a new userA Deep Learning-Based Approach to Extracting Periosteal and Endosteal Contours of Proximal Femur in Quantitative CT Images
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Automatic CT segmentation of proximal femur is crucial for the diagnosis and risk stratification of orthopedic diseases; however, current methods for the femur CT segmentation mainly rely on manual interactive segmentation, which is time-consuming and has limitations in both accuracy and reproducibility. In this study, we proposed an approach based on deep learning for the automatic extraction of the periosteal and endosteal contours of proximal femur in order to differentiate cortical and trabecular bone compartments. A three-dimensional (3D) end-to-end fully convolutional neural network, which can better combine the information between neighbor slices and get more accurate segmentation results, was developed for our segmentation task. 100 subjects aged from 50 to 87 years with 24,399 slices of proximal femur CT images were enrolled in this study. The separation of cortical and trabecular bone derived from the QCT software MIAF-Femur was used as the segmentation reference. We randomly divided the whole dataset into a training set with 85 subjects for 10-fold cross-validation and a test set with 15 subjects for evaluating the performance of models. Two models with the same network structures were trained and they achieved a dice similarity coefficient (DSC) of 97.87% and 96.49% for the periosteal and endosteal contours, respectively. To verify the excellent performance of our model for femoral segmentation, we measured the volume of different parts of the femur and compared it with the ground truth and the relative errors between predicted result and ground truth are all less than 5%. It demonstrated a strong potential for clinical use, including the hip fracture risk prediction and finite element analysis.
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Quantitative analysis of cell structures is essential for biomedical and pharmaceutical research. The standard imaging approach relies on fluorescence microscopy, where cell structures of interest are labeled by chemical staining techniques. However, these techniques are often invasive and sometimes even toxic to the cells, in addition to being time-consuming, labor-intensive, and expensive. Here, we introduce an alternative deep-learning-powered approach based on the analysis of brightfield images by a conditional generative adversarial neural network (cGAN). We show that this approach can extract information from the brightfield images to generate virtually-stained images, which can be used in subsequent downstream quantitative analyses of cell structures. Specifically, we train a cGAN to virtually stain lipid droplets, cytoplasm, and nuclei using brightfield images of human stem-cell-derived fat cells (adipocytes), which are of particular interest for nanomedicine and vaccine development. Subsequently, we use these virtually-stained images to extract quantitative measures about these cell structures. Generating virtually-stained fluorescence images is less invasive, less expensive, and more reproducible than standard chemical staining; furthermore, it frees up the fluorescence microscopy channels for other analytical probes, thus increasing the amount of information that can be extracted from each cell.
Magnetic resonance imaging (MRI) has been proposed as a complimentary method to measure bone quality and assess fracture risk. However, manual segmentation of MR images of bone is time-consuming, limiting the use of MRI measurements in the clinical practice. The purpose of this paper is to present an automatic proximal femur segmentation method that is based on deep convolutional neural networks (CNNs). This study had institutional review board approval and written informed consent was obtained from all subjects. A dataset of volumetric structural MR images of the proximal femur from 86 subject were manually-segmented by an expert. We performed experiments by training two different CNN architectures with multiple number of initial feature maps and layers, and tested their segmentation performance against the gold standard of manual segmentations using four-fold cross-validation. Automatic segmentation of the proximal femur achieved a high dice similarity score of 0.94$pm$0.05 with precision = 0.95$pm$0.02, and recall = 0.94$pm$0.08 using a CNN architecture based on 3D convolution exceeding the performance of 2D CNNs. The high segmentation accuracy provided by CNNs has the potential to help bring the use of structural MRI measurements of bone quality into clinical practice for management of osteoporosis.
CT imaging is crucial for diagnosis, assessment and staging COVID-19 infection. Follow-up scans every 3-5 days are often recommended for disease progression. It has been reported that bilateral and peripheral ground glass opacification (GGO) with or without consolidation are predominant CT findings in COVID-19 patients. However, due to lack of computerized quantification tools, only qualitative impression and rough description of infected areas are currently used in radiological reports. In this paper, a deep learning (DL)-based segmentation system is developed to automatically quantify infection regions of interest (ROIs) and their volumetric ratios w.r.t. the lung. The performance of the system was evaluated by comparing the automatically segmented infection regions with the manually-delineated ones on 300 chest CT scans of 300 COVID-19 patients. For fast manual delineation of training samples and possible manual intervention of automatic results, a human-in-the-loop (HITL) strategy has been adopted to assist radiologists for infection region segmentation, which dramatically reduced the total segmentation time to 4 minutes after 3 iterations of model updating. The average Dice simiarility coefficient showed 91.6% agreement between automatic and manual infaction segmentations, and the mean estimation error of percentage of infection (POI) was 0.3% for the whole lung. Finally, possible applications, including but not limited to analysis of follow-up CT scans and infection distributions in the lobes and segments correlated with clinical findings, were discussed.
Compressed sensing (CS) is a signal processing framework for efficiently reconstructing a signal from a small number of measurements, obtained by linear projections of the signal. Block-based CS is a lightweight CS approach that is mostly suitable for processing very high-dimensional images and videos: it operates on local patches, employs a low-complexity reconstruction operator and requires significantly less memory to store the sensing matrix. In this paper we present a deep learning approach for block-based CS, in which a fully-connected network performs both the block-based linear sensing and non-linear reconstruction stages. During the training phase, the sensing matrix and the non-linear reconstruction operator are emph{jointly} optimized, and the proposed approach outperforms state-of-the-art both in terms of reconstruction quality and computation time. For example, at a 25% sensing rate the average PSNR advantage is 0.77dB and computation time is over 200-times faster.
Acute aortic syndrome (AAS) is a group of life threatening conditions of the aorta. We have developed an end-to-end automatic approach to detect AAS in computed tomography (CT) images. Our approach consists of two steps. At first, we extract N cross sections along the segmented aorta centerline for each CT scan. These cross sections are stacked together to form a new volume which is then classified using two different classifiers, a 3D convolutional neural network (3D CNN) and a multiple instance learning (MIL). We trained, validated, and compared two models on 2291 contrast CT volumes. We tested on a set aside cohort of 230 normal and 50 positive CT volumes. Our models detected AAS with an Area under Receiver Operating Characteristic curve (AUC) of 0.965 and 0.985 using 3DCNN and MIL, respectively.
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