Liver Tissue Classification Using an Auto-context-based Deep Neural Network with a Multi-phase Training Framework.

In this project, our goal is to classify different types of liver tissue on 3D multi-parameter magnetic resonance images in patients with hepatocellular carcinoma. In these cases, 3D fully annotated segmentation masks from experts are expensive to acquire, thus the dataset available for training a predictive model is usually small. To achieve the goal, we designed a novel deep convolutional neural network that incorporates auto-context elements directly into a U-net-like architecture. We used a patch-based strategy with a weighted sampling procedure in order to train on a sufficient number of samples. Furthermore, we designed a multi-resolution and multi-phase training framework to reduce the learning space and to increase the regularization of the model. Our method was tested on images from 20 patients and yielded promising results, outperforming standard neural network approaches as well as a benchmark method for liver tissue classification.

C-arm cone-beam computed tomography in interventional oncology: technical aspects and clinical applications.

C-arm cone-beam computed tomography (CBCT) is a new imaging technology integrated in modern angiographic systems. Due to its ability to obtain cross-sectional imaging and the possibility to use dedicated planning and navigation software, it provides an informed platform for interventional oncology procedures. In this paper, we highlight the technical aspects and clinical applications of CBCT imaging and navigation in the most common loco-regional oncological treatments.

Transcatheter arterial embolization in patients with kidney diseases: an overview of the technical aspects and clinical indications.

Therapeutic embolization is defined as the voluntary occlusion of one or several vessels, and this is achieved by inserting material into the lumen to obtain transient or permanent thrombosis in the downstream vascular bed. There are a number of indications for this approach in urological practice, in particular for the patients with parenchymatous or vascular kidney disease. In this review, we present the different embolization techniques and the principally employed occluding agents, and then we present the principal clinical indications and we discuss other pathologies that may benefit from this non-invasive therapy. The complications, side effects and main precautions associated with this approach are also described.

Embolization of acute nonvariceal upper gastrointestinal hemorrhage resistant to endoscopic treatment: results and predictors of recurrent bleeding.

Acute nonvariceal upper gastrointestinal (UGI) hemorrhage is a frequent complication associated with significant morbidity and mortality. The most common cause of UGI bleeding is peptic ulcer disease, but the differential diagnosis is diverse and includes tumors; ischemia; gastritis; arteriovenous malformations, such as Dieulafoy lesions; Mallory-Weiss tears; trauma; and iatrogenic causes. Aggressive treatment with early endoscopic hemostasis is essential for a favorable outcome. However, severe bleeding despite conservative medical treatment or endoscopic intervention occurs in 5-10% of patients, requiring surgery or transcatheter arterial embolization. Surgical intervention is usually an expeditious and gratifying endeavor, but it can be associated with high operative mortality rates. Endovascular management using superselective catheterization of the culprit vessel, «sandwich¼ occlusion, or blind embolization has emerged as an alternative to emergent operative intervention for high-risk patients and is now considered the first-line therapy for massive UGI bleeding refractory to endoscopic treatment. Indeed, many published studies have confirmed the feasibility of this approach and its high technical and clinical success rates, which range from 69 to 100% and from 63 to 97%, respectively, even if the choice of the best embolic agent among coils, cyanaocrylate glue, gelatin sponge, or calibrated particles remains a matter of debate. However, factors influencing clinical outcome, especially predictors of early rebleeding, are poorly understood, and few studies have addressed this issue. This review of the literature will attempt to define the role of embolotherapy for acute nonvariceal UGI hemorrhage that fails to respond to endoscopic hemostasis and to summarize data on factors predicting angiographic and embolization failure.

Oxidative DNA damage in osteoarthritic porcine articular cartilage.

Osteoarthritis (OA) is associated with increased levels of reactive oxygen species. This study investigated if increased oxidative DNA damage accumulates in OA articular cartilage compared with non-OA articular cartilage from pigs with spontaneous OA. Additionally, the ability of nitric oxide (NO) or peroxynitrite (ONOO(-)) induced DNA damage in non-OA chondrocytes to undergo endogenous repair was investigated. Porcine femoral condyles were graded for the stage of OA, macroscopically by the Collins Scale, and histologically by the modified Mankin Grade. Levels of DNA damage were determined in non-OA and OA cartilage, using the comet assay. For calibration, DNA damage was measured by exposing non-OA chondrocytes to 0-12 Gray (Gy) of X-ray irradiation. Non-OA articular chondrocytes were treated with 0-500 microM of NO donors (NOC-18 or SIN-1), and DNA damage assessed after treatment and 5 days recovery. A significant increase (P < 0.01) in oxidative DNA damage occurred in OA chondrocytes in joints with Mankin Grades 3 or greater, compared to non-OA chondrocytes. The percentage of nuclei containing DNA damage increased significantly (P < 0.001) from early to late grades of OA. An increase of approximately 0.65-1.7 breaks/1,000 kb of DNA occurred in OA, compared to non-OA nuclei. NOC-18 or SIN-1 caused significant DNA damage (P < 0.001) in non-OA chondrocytes that did not undergo full endogenous repair after 5 days (P < 0.05). Our data suggest significant levels of oxidative DNA damage occur in OA chondrocytes that accumulates with OA progression. Additionally, DNA damage induced by NO and ONOO(-) in non-OA chondrocytes does not undergo full endogenous repair.

Application of MOSFET detectors for dosimetry in small animal radiography using short exposure times.

Digital subtraction angiography (DSA) X-ray imaging for small animals can be used for functional phenotyping given its ability to capture rapid physiological changes at high spatial and temporal resolution. The higher temporal and spatial requirements for small-animal imaging drive the need for short, high-flux X-ray pulses. However, high doses of ionizing radiation can affect the physiology. The purpose of this study was to verify and apply metal oxide semiconductor field effect transistor (MOSFET) technology to dosimetry for small-animal diagnostic imaging. A tungsten anode X-ray source was used to expose a tissue-equivalent mouse phantom. Dose measurements were made on the phantom surface and interior. The MOSFETs were verified with thermoluminescence dosimeters (TLDs). Bland-Altman analysis showed that the MOSFET results agreed with the TLD results (bias, 0.0625). Using typical small animal DSA scan parameters, the dose ranged from 0.7 to 2.2 cGy. Application of the MOSFETs in the small animal environment provided two main benefits: (1) the availability of results in near real-time instead of the hours needed for TLD processes and (2) the ability to support multiple exposures with different X-ray techniques (various of kVp, mA and ms) using the same MOSFET. This MOSFET technology has proven to be a fast, reliable small animal dosimetry method for DSA imaging and is a good system for dose monitoring for serial and gene expression studies.

A high-precision contrast injector for small animal x-ray digital subtraction angiography.

The availability of genetically altered animal models of human disease for basic research has generated great interest in new imaging methodologies. Digital subtraction angiography (DSA) offers an appealing approach to functional imaging in small animals because of the high spatial and temporal resolution, and the ability to visualize and measure blood flow. The micro-injector described here meets crucial performance parameters to ensure optimal vessel enhancement without significantly increasing the total blood volume or producing overlap of enhanced structures. The micro-injector can inject small, reproducible volumes of contrast agent at high flow rates with computer-controlled timing synchronized to cardiopulmonary activity. Iterative bench-top and live animal experiments with both rat and mouse have been conducted to evaluate the performance of this computer-controlled micro-injector, a first demonstration of a new device designed explicitly for the unique requirements of DSA in small animals. Injection protocols were optimized and screened for potential physiological impact. For the optimized protocols, we found that changes in the time-density curves for representative regions of interest in the thorax were due primarily to physiological changes, independent of micro-injector parameters.

Pulmonary perfusion imaging in the rodent lung using dynamic contrast-enhanced MRI.

With the development of various models of pulmonary disease, there is tremendous interest in quantitative regional assessment of pulmonary function. While ventilation imaging has been addressed to a certain extent, perfusion imaging for small animals has not kept pace. In humans and large animals perfusion can be assessed using dynamic contrast-enhanced (DCE) MRI with a single bolus injection of a gadolinium (Gd)-based contrast agent. But the method developed for the clinic cannot be translated directly to image the rodent due to the combined requirements of higher spatial and temporal resolution. This work describes a novel image acquisition technique staggered over multiple, repeatable bolus injections of contrast agent using an automated microinjector, synchronized with image acquisition to achieve dynamic first-pass contrast enhancement in the rat lung. This allows dynamic first-pass imaging that can be used to quantify pulmonary perfusion. Further improvements are made in the spatial and temporal resolution by combining the multiple injection acquisition method with Interleaved Radial Imaging and "Sliding window-keyhole" reconstruction (IRIS). The results demonstrate a simultaneous increase in spatial resolution (<200 mum) and temporal resolution (<200 ms) over previous methods, with a limited loss in signal-to-noise-ratio.

Tomographic digital subtraction angiography for lung perfusion estimation in rodents.

In vivo measurements of perfusion present a challenge to existing small animal imaging techniques such as magnetic resonance microscopy, micro computed tomography, micro positron emission tomography, and microSPECT, due to combined requirements for high spatial and temporal resolution. We demonstrate the use of tomographic digital subtraction angiography (TDSA) for estimation of perfusion in small animals. TDSA augments conventional digital subtraction angiography (DSA) by providing three-dimensional spatial information using tomosynthesis algorithms. TDSA is based on the novel paradigm that the same time density curves can be reproduced in a number of consecutive injections of microL volumes of contrast at a series of different angles of rotation. The capabilities of TDSA are established in studies on lung perfusion in rats. Using an imaging system developed in-house, we acquired data for four-dimensional (4D) imaging with temporal resolution of 140 ms, in-plane spatial resolution of 100 microm, and slice thickness on the order of millimeters. Based on a structured experimental approach, we optimized TDSA imaging providing a good trade-off between slice thickness, the number of injections, contrast to noise, and immunity to artifacts. Both DSA and TDSA images were used to create parametric maps of perfusion. TDSA imaging has potential application in a number of areas where functional perfusion measurements in 4D can provide valuable insight into animal models of disease and response to therapeutics.

Tumor imaging in small animals with a combined micro-CT/micro-DSA system using iodinated conventional and blood pool contrast agents.

X-ray based micro-computed tomography (CT) and micro-digital subtraction angiography (DSA) are important non-invasive imaging modalities for following tumorogenesis in small animals. To exploit these imaging capabilities further, the two modalities were combined into a single system to provide both morphological and functional data from the same tumor in a single imaging session. The system is described and examples are given of imaging implanted fibrosarcoma tumors in rats using two types of contrast media: (a) a new generation of blood pool contrast agent containing iodine with a concentration of 130 mg/mL (Fenestratrade mark VC, Alerion Biomedical, San Diego, CA, USA) for micro-CT and (b) a conventional iodinated contrast agent (Isovue(R)-370 mg/mL iodine, trademark of Bracco Diagnostics, Princeton, NJ, USA) for micro-DSA. With the blood pool contrast agent, the 3D vascular architecture is revealed in exquisite detail at 100 microm resolution. Micro-DSA images, in perfect registration with the 3D micro-CT datasets, provide complementary functional information such as mean transit times and relative blood flow through the tumor. This imaging approach could be used to understand tumor angiogenesis better and be the basis for evaluating anti-angiogenic therapies.