Performance evaluation of a micro-CT system for laboratory animal imaging with iterative reconstruction capabilities.

BACKGROUND: In recent years, there has been a rapid proliferation in micro-computed tomography (micro-CT) systems becoming more available for routine preclinical research, with applications in many areas, including bone, lung, cancer, and cardiac imaging. Micro-CT provides the means to non-invasively acquire detailed anatomical information, but high-resolution imaging comes at the cost of longer scan times and higher doses, which is not desirable given the potential risks related to x-ray radiation. To achieve dose reduction and higher throughputs without compromising image quality, fewer projections can be acquired. This is where iterative reconstruction methods can have the potential to reduce noise since these algorithms can better handle sparse projection data, compared to filtered backprojection PURPOSE: We evaluate the performance characteristics of a compact benchtop micro-CT scanner that provides iterative reconstruction capabilities with GPU-based acceleration. We thereby investigate the potential benefit of iterative reconstruction for dose reduction. METHODS: Based on a series of phantom experiments, the benchtop micro-CT system was characterized in terms of image uniformity, noise, low contrast detectability, linearity, and spatial resolution. Whole-body images of a plasticized ex vivo mouse phantom were also acquired. Different acquisition protocols (general-purpose versus high-resolution, including low dose scans) and different reconstruction strategies (analytic versus iterative algorithms: FDK, ISRA, ISRA-TV) were compared. RESULTS: Signal uniformity was maintained across the radial and axial field-of-view (no cupping effect) with an average difference in Hounsfield units (HU) between peripheral and central regions below 50. For low contrast detectability, regions with at least ∆HU of 40 to surrounding material could be discriminated (for rods of 2.5 mm diameter). A high linear correlation (R2  = 0.997) was found between measured CT values and iodine concentrations (0-40 mg/ml). Modulation transfer function (MTF) calculations on a wire phantom evaluated a resolution of 10.2 lp/mm at 10% MTF that was consistent with the 8.3% MTF measured on the 50 µm bars (10 lp/mm) of a bar-pattern phantom. Noteworthy changes in signal-to-noise and contrast-to-noise values were found for different acquisition and reconstruction protocols. Our results further showed the potential of iterative reconstruction to deliver images with less noise and artefacts. CONCLUSIONS: In summary, the micro-CT system that was evaluated in the present work was shown to provide a good combination of performance characteristics between image uniformity, low contrast detectability, and resolution in short scan times. With the iterative reconstruction capabilities of this micro-CT system in mind (ISRA and ISRA-TV), the adoption of such algorithms by GPU-based acceleration enables the integration of noise reduction methods which here demonstrated potential for high-quality imaging at reduced doses.

Data Curation for Preclinical and Clinical Multimodal Imaging Studies.

PURPOSE: In biomedical research, imaging modalities help discover pathological mechanisms to develop and evaluate novel diagnostic and theranostic approaches. However, while standards for data storage in the clinical medical imaging field exist, data curation standards for biomedical research are yet to be established. This work aimed at developing a free secure file format for multimodal imaging studies, supporting common in vivo imaging modalities up to five dimensions as a step towards establishing data curation standards for biomedical research. PROCEDURES: Images are compressed using lossless compression algorithm. Cryptographic hashes are computed on the compressed image slices. The hashes and compressions are computed in parallel, speeding up computations depending on the number of available cores. Then, the hashed images with digitally signed timestamps are cryptographically written to file. Fields in the structure, compressed slices, hashes, and timestamps are serialized for writing and reading from files. The C++ implementation is tested on multimodal data from six imaging sites, well-documented, and integrated into a preclinical image analysis software. RESULTS: The format has been tested with several imaging modalities including fluorescence molecular tomography/x-ray computed tomography (CT), positron emission tomography (PET)/CT, single-photon emission computed tomography/CT, and PET/magnetic resonance imaging. To assess performance, we measured the compression rate, ratio, and time spent in compression. Additionally, the time and rate of writing and reading on a network drive were measured. Our findings demonstrate that we achieve close to 50 % reduction in storage space for µCT data. The parallelization speeds up the hash computations by a factor of 4. We achieve a compression rate of 137 MB/s for file of size 354 MB. CONCLUSIONS: The development of this file format is a step to abstract and curate common processes involved in preclinical and clinical multimodal imaging studies in a standardized way. This work also defines better interface between multimodal imaging modalities and analysis software.

Angiopoietin-2 Promotes Pathological Angiogenesis and Is a Therapeutic Target in Murine Nonalcoholic Fatty Liver Disease.

Angiogenesis contributes to the development of nonalcoholic steatohepatitis (NASH) and promotes inflammation, fibrosis, and progression to hepatocellular carcinoma (HCC). Angiopoietin-2 (Ang-2) is a key regulator of angiogenesis. We aimed to investigate the role of Ang-2 and its potential as a therapeutic target in NASH using human samples, in vivo mouse models, and in vitro assays. Serum Ang-2 levels were determined in 104 obese patients undergoing bariatric surgery and concomitant liver biopsy. The effect of the Ang-2/Tie2 receptor inhibiting peptibody L1-10 was evaluated in the methionine-choline deficient (MCD) and streptozotocin-western diet nonalcoholic fatty liver disease mouse models, and in vitro on endothelial cells and bone marrow-derived macrophages. The hepatic vasculature was visualized with µCT scans and scanning electron microscopy of vascular casts. Serum Ang-2 levels were increased in patients with histological NASH compared with patients with simple steatosis and correlated with hepatic CD34 immunoreactivity as a marker of hepatic angiogenesis. Serum and hepatic Ang-2 levels were similarly increased in mice with steatohepatitis. Both preventive and therapeutic L1-10 treatment reduced hepatocyte ballooning and fibrosis in MCD diet-fed mice and was associated with reduced hepatic angiogenesis and normalization of the vascular micro-architecture. Liver-isolated endothelial cells and monocytes from MCD-fed L1-10-treated mice showed reduced expression of leukocyte adhesion and inflammatory markers, respectively, compared with cells from untreated MCD diet-fed mice. In the streptozotocin-western diet model, therapeutic Ang-2 inhibition was able to reverse NASH and attenuate HCC progression. In vitro, L1-10 treatment mitigated increased cytokine production in lipopolysaccharide-stimulated endothelial cells but not in macrophages. Conclusion: Our findings provide evidence for Ang-2 inhibition as a therapeutic strategy to target pathological angiogenesis in NASH.

Species-dependent extracranial manifestations of a brain seeking breast cancer cell line.

PURPOSE: Metastatic brain tumors pose a severe problem in the treatment of patients with breast carcinoma. Preclinical models have been shown to play an important role in unraveling the underlying mechanisms behind the metastatic process and evaluation of new therapeutic approaches. As the size of the rat brain allows improved in vivo imaging, we attempted to establish a rat model for breast cancer brain metastasis that allows follow-up by 7 tesla (7T) preclinical Magnetic Resonance Imaging (MRI). PROCEDURES: Green fluorescent protein-transduced (eGFP) MDA-MB-231br breast cancer cells were labeled with micron-sized particles of iron oxide (MPIOs) and intracardially injected in the left ventricle of female nude rats and mice. 7T preclinical MRI was performed to show the initial distribution of MPIO-labeled cancer cells and to visualize metastasis in the brain. Occurrence of potential metastasis outside the brain was evaluated by 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) positron emission tomography (PET)/computed tomography (CT) and potential bone lesions were assessed using [18F]sodium fluoride ([18F]NaF) PET/CT. RESULTS: The first signs of brain metastasis development were visible as hyperintensities on T2-weighted (T2w) MR images acquired 3 weeks after intracardiac injection in rats and mice. Early formation of unexpected bone metastasis in rats was clinically observed and assessed using PET/CT. Almost no bone metastasis development was observed in mice after PET/CT evaluation. CONCLUSIONS: Our results suggest that the metastatic propensity of the MDA-MB-231br/eGFP cancer cell line outside the brain is species-dependent. Because of early and abundant formation of bone metastasis with the MDA-MB-231br/eGFP cancer cell line, this rat model is currently not suitable for investigating brain metastasis as a single disease model nor for evaluation of novel brain metastasis treatment strategies.

Vulnerable plaque detection and quantification with gold particle-enhanced computed tomography in atherosclerotic mouse models.

Recently, an apolipoprotein E-deficient (ApoE-/-) mouse model with a mutation (C1039G+/-) in the fibrillin-1 (Fbn1) gene (ApoE-/-Fbn1C1039G+/- mouse model) was developed showing vulnerable atherosclerotic plaques, prone to rupture, in contrast to the ApoE-/- mouse model, where mainly stable plaques are present. One indicator of plaque vulnerability is the level of macrophage infiltration. Therefore, this study aimed to measure and quantify in vivo the macrophage infiltration related to plaque development and progression. For this purpose, 5-weekly consecutive gold nanoparticle-enhanced micro-computed tomography (microCT) scans were acquired. Histology confirmed that the presence of contrast agent coincided with the presence of macrophages. Based on the microCT scans, regions of the artery wall with contrast agent present were calculated and visualized in three dimensions. From this information, the contrast-enhanced area and contrast-enhanced centerline length were calculated for the branches of the carotid bifurcation (common, external, and internal carotid arteries). Statistical analysis showed a more rapid development and a larger extent of plaques in the ApoE-/-Fbn1C1039G+/- compared to the ApoE-/- mice. Regional differences between the branches were also observable and quantifiable. We developed and applied a methodology based on gold particle-enhanced microCT to visualize the presence of macrophages in atherosclerotic plaques in vivo.

Evaluation of Fisher Information Matrix-Based Methods for Fast Assessment of Image Quality in Pinhole SPECT.

The accurate determination of the local impulse response and the covariance in voxels from penalized maximum likelihood reconstructed images requires performing reconstructions from many noise realizations of the projection data. As this is usually a very time-consuming process, efficient analytical approximations based on the Fisher information matrix (FIM) have been extensively used in PET and SPECT to estimate these quantities. For 3D imaging, however, additional approximations need to be made to the FIM in order to speed up the calculations. The most common approach is to use the local shift-invariant (LSI) approximation of the FIM, but this assumes specific conditions which are not always necessarily valid. In this paper we take a single-pinhole SPECT system and compare the accuracy of the LSI approximation against two other methods that have been more recently put forward: the non-uniform object-space pixelation (NUOP) and the subsampled FIM. These methods do not assume such restrictive conditions while still increasing the speed of the calculations considerably. Our results indicate that in pinhole SPECT the NUOP and subsampled FIM approaches could be more reliable than the LSI approximation, especially when a high accuracy is required.

Use of a ray-based reconstruction algorithm to accurately quantify preclinical microSPECT images.

This work aimed to measure the in vivo quantification errors obtained when ray-based iterative reconstruction is used in micro-single-photon emission computed tomography (SPECT). This was investigated with an extensive phantom-based evaluation and two typical in vivo studies using 99mTc and 111In, measured on a commercially available cadmium zinc telluride (CZT)-based small-animal scanner. Iterative reconstruction was implemented on the GPU using ray tracing, including (1) scatter correction, (2) computed tomography-based attenuation correction, (3) resolution recovery, and (4) edge-preserving smoothing. It was validated using a National Electrical Manufacturers Association (NEMA) phantom. The in vivo quantification error was determined for two radiotracers: [99mTc]DMSA in naive mice (n  =  10 kidneys) and [111In]octreotide in mice (n  =  6) inoculated with a xenograft neuroendocrine tumor (NCI-H727). The measured energy resolution is 5.3% for 140.51 keV (99mTc), 4.8% for 171.30 keV, and 3.3% for 245.39 keV (111In). For 99mTc, an uncorrected quantification error of 28 ± 3% is reduced to 8 ± 3%. For 111In, the error reduces from 26 ± 14% to 6 ± 22%. The in vivo error obtained with 99mTc-dimercaptosuccinic acid ([99mTc]DMSA) is reduced from 16.2 ± 2.8% to -0.3 ± 2.1% and from 16.7 ± 10.1% to 2.2 ± 10.6% with [111In]octreotide. Absolute quantitative in vivo SPECT is possible without explicit system matrix measurements. An absolute in vivo quantification error smaller than 5% was achieved and exemplified for both [99mTc]DMSA and [111In]octreotide.

Absence of cardiovascular manifestations in a haploinsufficient Tgfbr1 mouse model.

Loeys-Dietz syndrome (LDS) is an autosomal dominant arterial aneurysm disease belonging to the spectrum of transforming growth factor ß (TGFß)-associated vasculopathies. In its most typical form it is characterized by the presence of hypertelorism, bifid uvula/cleft palate and aortic aneurysm and/or arterial tortuosity. LDS is caused by heterozygous loss of function mutations in the genes encoding TGFß receptor 1 and 2 (TGFBR1 and -2), which lead to a paradoxical increase in TGFß signaling. To address this apparent paradox and to gain more insight into the pathophysiology of aneurysmal disease, we characterized a new Tgfbr1 mouse model carrying a p.Y378* nonsense mutation. Study of the natural history in this model showed that homozygous mutant mice die during embryonic development due to defective vascularization. Heterozygous mutant mice aged 6 and 12 months were morphologically and (immuno)histochemically indistinguishable from wild-type mice. We show that the mutant allele is degraded by nonsense mediated mRNA decay, expected to result in haploinsufficiency of the mutant allele. Since this haploinsufficiency model does not result in cardiovascular malformations, it does not allow further study of the process of aneurysm formation. In addition to providing a comprehensive method for cardiovascular phenotyping in mice, the results of this study confirm that haploinsuffciency is not the underlying genetic mechanism in human LDS.

Design and performance of a compact and stationary microSPECT system.

PURPOSE: Over the last ten years, there has been an extensive growth in the development of microSPECT imagers. Most of the systems are based on the combination of conventional, relatively large gamma cameras with poor intrinsic spatial resolution and multipinhole collimators working in large magnification mode. Spatial resolutions range from 0.58 to 0.76 mm while peak sensitivities vary from 0.06% to 0.4%. While pushing the limits of performance is of major importance, the authors believe that there is a need for smaller and less complex systems that bring along a reduced cost. While low footprint and low-cost systems can make microSPECT available to more researchers, the ease of operation and calibration and low maintenance cost are additional factors that can facilitate the use of microSPECT in molecular imaging. In this paper, the authors simulate the performance of a microSPECT imager that combines high space-bandwidth detectors and pinholes with truncated projection, resulting in a small and stationary system. METHODS: A system optimization algorithm is used to determine the optimal SPECT systems, given our high resolutions detectors and a fixed field-of-view. These optimal system geometries are then used to simulate a Defrise disk phantom and a hot rod phantom. Finally, a MOBY mouse phantom, with realistic concentrations of Tc99m-tetrofosmin is simulated. RESULTS: Results show that the authors can successfully reconstruct a Defrise disk phantom of 24 mm in diameter without any rotating system components or translation of the object. Reconstructed spatial resolution is approximately 800 µm while the peak sensitivity is 0.23%. Finally, the simulation of the MOBY mouse phantom shows that the authors can accurately reconstruct mouse images. CONCLUSIONS: These results show that pinholes with truncated projections can be used in small magnification or minification mode to obtain a compact and stationary microSPECT system. The authors showed that they can reach state-of-the-art system performance and can successfully reconstruct images with realistic noise levels in a preclinical context. Such a system can be useful for dynamic SPECT imaging.

Design and simulation of a full-ring multi-lofthole collimator for brain SPECT.

Currently, clinical brain single photon emission computed tomography (SPECT) is mostly performed using rotating dual-head gamma cameras equipped with low-energy-high-resolution parallel-beam collimators (LEHR PAR). The resolution of these systems is rather poor (8-10 mm) and the rotation of the heavy gamma cameras can introduce misalignment errors. Therefore, we designed a static full-ring multi-lofthole brain SPECT insert for an existing ring of LaBr3 (5% Ce) detectors. The novelty of the design is found in the shutter mechanism that makes the system very flexible and eliminates the need for rotating parts. A stationary SPECT insert is not only more robust, it is also easier to integrate in a magnetic resonance imaging system (MRI) for simultaneous SPECT-MRI. The target spatial resolution of our design is 6 mm. In this study we used analytical calculations to optimize the collimator for an existing ring of LaBr3 (5% Ce) detectors. We fixed the target spatial resolution at 6 mm in the center of the field-of-view and maximized the volume sensitivity by changing the collimator radius, the aperture and the number of loftholes. Based on these optimal parameters we simulated phantom data and evaluated the image quality of our multi-lofthole system. We simulated a noiseless uniform and Defrise phantom to assess artifacts and sampling completeness and a noiseless hot-rod phantom to assess the reconstructed spatial resolution. We visually evaluated a simulated noisy Hoffman phantom with two lesions. Then, we evaluated the non-prewhitening matched filter signal-to-noise ratio (NPW-SNR) in two lesion detectability phantoms: one with hot lesions and one with cold lesions. Finally, a contrast-to-noise (CNR) study was performed on a phantom with both hot and cold lesions of different sizes (6-16 mm). All results were compared to a LEHR PAR system. The optimization resulted in a final collimator design with a volume sensitivity of 1.55 × 10(-4) cps Bq(-1), which is 2.5 times lower than the sensitivity of a dual-head system with LEHR PAR collimators. Spatial resolution, on the other hand, has clearly improved compared to LEHR PAR: with the multi-lofthole system we successfully reconstructed 4 mm hot rods. Although this improved resolution did not result in an unambiguous improvement in CNR or NPW-SNR, we believe that the flexibility of the shutter mechanism opens interesting perspectives toward time-multiplexing and integration with MRI.

Low-dose micro-CT imaging for vascular segmentation and analysis using sparse-view acquisitions.

The aim of this study is to investigate whether reliable and accurate 3D geometrical models of the murine aortic arch can be constructed from sparse-view data in vivo micro-CT acquisitions. This would considerably reduce acquisition time and X-ray dose. In vivo contrast-enhanced micro-CT datasets were reconstructed using a conventional filtered back projection algorithm (FDK), the image space reconstruction algorithm (ISRA) and total variation regularized ISRA (ISRA-TV). The reconstructed images were then semi-automatically segmented. Segmentations of high- and low-dose protocols were compared and evaluated based on voxel classification, 3D model diameters and centerline differences. FDK reconstruction does not lead to accurate segmentation in the case of low-view acquisitions. ISRA manages accurate segmentation with 1024 or more projection views. ISRA-TV needs a minimum of 256 views. These results indicate that accurate vascular models can be obtained from micro-CT scans with 8 times less X-ray dose and acquisition time, as long as regularized iterative reconstruction is used.

Replacing vascular corrosion casting by in vivo micro-CT imaging for building 3D cardiovascular models in mice.

PURPOSE: The purpose of this study was to investigate if in vivo micro-computed tomography (CT) is a reliable alternative to micro-CT scanning of a vascular corrosion cast. This would allow one to study the early development of cardiovascular diseases. PROCEDURES: Datasets using both modalities were acquired, segmented, and used to generate a 3D geometrical model from nine mice. As blood pool contrast agent, Fenestra VC-131 was used. Batson's No. 17 was used as casting agent. Computational fluid dynamics simulations were performed on both datasets to quantify the difference in wall shear stress (WSS). RESULTS: Aortic arch diameters show 30% to 40% difference between the Fenestra VC-131 and the casted dataset. The aortic arch bifurcation angles show less than 20% difference between both datasets. Numerically computed WSS showed a 28% difference between both datasets. CONCLUSIONS: Our results indicate that in vivo micro-CT imaging can provide an excellent alternative for vascular corrosion casting. This enables follow-up studies.

Kinetics of angiogenic changes in a new mouse model for hepatocellular carcinoma.

BACKGROUND: The increasing incidence of hepatocellular carcinoma in Western countries has led to an expanding interest of scientific research in this field. Therefore, a vast need of experimental models that mimic the natural pathogenesis of hepatocellular carcinoma (HCC) in a short time period is present. The goal of our study was (1) to develop an efficient mouse model for HCC research, in which tumours develop in a natural background of fibrosis and (2) to assess the time-dependent angiogenic changes in the pathogenesis of HCC. METHODS: Weekly intraperitoneal injections with the hepatocarcinogenic compound N-nitrosodiethylamine was applied as induction method and samples were taken at several time points to assess the angiogenic changes during the progression of HCC. RESULTS: The N-nitrosodiethylamine-induced mouse model provides well vascularised orthotopic tumours after 25 weeks. It is a representative model for human HCC and can serve as an excellent platform for the development of new therapeutic targets.