Preclinical micro-CT Research Articles

3D whole body preclinical micro-CT database of subcutaneous tumors in mice with annotations from 3 annotators

A pivotal animal model for development of anticancer molecules is mice with subcutaneous tumors, grown by injection of xenografted tumor cells, where micro-Computed Tomography (µCT) of the mice is used to analyze the efficacy of the anticancer molecule. Manual delineation of the tumor region is necessary for the analysis, which is time-consuming and inconsistent, highlighting the need for automatic segmentation (AS) tools. This study introduces a preclinical µCT database, comprising 452 whole-body scans from 223 individual mice with subcutaneous tumors, spanning ten diverse µCT datasets conducted between 2014 and 2020 on a preclinical PET/CT scanner, making it the hitherto largest dataset of its kind. Each tumor is annotated manually by three expert annotators, allowing for robust model development. Inter-annotator agreement was analyzed, and we report an overall annotation agreement of 0.903 ± 0.046 (mean ± std) Fleiss’ Kappa and a mean deviation in volume estimation of 0.015 ± 0.010 cm3 (6.9% ± 4.7), which establishes a human baseline accuracy for delineation of subcutaneous tumors, while showing good inter-annotator agreement.

Quantitative multi-energy micro-CT: A simulation and phantom study for simultaneous imaging of four different contrast materials using an energy integrating detector

Emerging from the development of single-energy Computed Tomography (CT) and Dual-Energy Computed Tomography, Multi-Energy Computed Tomography (MECT) is a promising tool allowing advanced material and tissue decomposition and thereby enabling the use of multiple contrast materials in preclinical research.The scope of this work was to evaluate whether a usual preclinical micro-CT system is applicable for the decomposition of different materials using MECT together with a matrix-inversion method and how different changes of the measurement-environment affect the results.A matrix-inversion based algorithm to differentiate up to five materials (iodine, iron, barium, gadolinium, residual material) by applying four different acceleration voltages/energy levels was established. We carried out simulations using different ratios and concentrations (given in fractions of volume units, VU) of the four different materials (plus residual material) at different noise-levels for 30 keV, 40 keV, 50 keV, 60 keV, 80 keV and 100 keV (monochromatic). Our simulation results were then confirmed by using region of interest-based measurements in a phantom-study at corresponding acceleration voltages. Therefore, different mixtures of contrast materials were scanned using a micro-CT. Voxel wise evaluation of the phantom imaging data was conducted to confirm its usability for future imaging applications and to estimate the influence of varying noise-levels, scattering, artifacts and concentrations.The analysis of our simulations showed the smallest deviation of 0.01 (0.003–0.15) VU between given and calculated concentrations of the different contrast materials when using an energy-combination of 30 keV, 40 keV, 50 keV and 100 keV for MECT. Subsequent MECT phantom measurements, however, revealed a combination of acceleration voltages of 30 kV, 40 kV, 60 kV and 100 kV as most effective for performing material decomposition with a deviation of 0.28 (0–1.07) mg/ml. The feasibility of our voxelwise analyses using the proposed algorithm was then confirmed by the generation of phantom parameter-maps that matched the known contrast material concentrations. The results were mostly influenced by the noise-level and the concentrations used in the phantoms.MECT using a standard micro-CT combined with a matrix inversion method is feasible at four different imaging energies and allows the differentiation of mixtures of up to four contrast materials plus an additional residual material.

Application-specific approaches to MicroCT for evaluation of mouse models of pulmonary disease.

The advent of micro-computed tomography (microCT) has provided significant advancement in our ability to generate clinically relevant assessments of lung health and disease in small animal models. As microCT use to generate outcomes analysis in pulmonary preclinical models has increased there have been substantial improvements in image quality and resolution, and data analysis software. However, there are limited published methods for standardized imaging and automated analysis available for investigators. Manual quantitative analysis of microCT images is complicated by the presence of inflammation and parenchymal disease. To improve the efficiency and limit user-associated bias, we have developed an automated pulmonary air and tissue segmentation (PATS) task list to segment lung air volume and lung tissue volume for quantitative analysis. We demonstrate the effective use of the PATS task list using four distinct methods for imaging, 1) in vivo respiration controlled scanning using a flexiVent, 2) longitudinal breath-gated in vivo scanning in resolving and non-resolving pulmonary disease initiated by lipopolysaccharide-, bleomycin-, and silica-exposure, 3) post-mortem imaging, and 4) ex vivo high-resolution scanning. The accuracy of the PATS task list was compared to manual segmentation. The use of these imaging techniques and automated quantification methodology across multiple models of lung injury and fibrosis demonstrates the broad applicability and adaptability of microCT to various lung diseases and small animal models and presents a significant advance in efficiency and standardization of preclinical microCT imaging and analysis for the field of pulmonary research.

Ultrahigh resolution whole body photon counting computed tomography as a novel versatile tool for translational research from mouse to man

X-ray computed tomography (CT) is a cardinal tool in clinical practice. It provides cross-sectional images within seconds. The recent introduction of clinical photon-counting CT allowed for an increase in spatial resolution by more than a factor of two resulting in a pixel size in the center of rotation of about 150 µm. This level of spatial resolution is in the order of dedicated preclinical micro-CT systems. However so far, the need for different dedicated clinical and preclinical systems often hinders the rapid translation of early research results to applications in men. This drawback might be overcome by ultra-high resolution (UHR) clinical photon-counting CT unifying preclinical and clinical research capabilities in a single machine. Herein, the prototype of a clinical UHR PCD CT (SOMATOM CounT, Siemens Healthineers, Forchheim, Germany) was used. The system comprises a conventional energy-integrating detector (EID) and a novel photon-counting detector (PCD). While the EID provides a pixel size of 0.6 mm in the centre of rotation, the PCD provides a pixel size of 0.25 mm. Additionally, it provides a quantification of photon energies by sorting them into up to four distinct energy bins. This acquisition of multi-energy data allows for a multitude of applications, e.g. pseudo-monochromatic imaging. In particular, we examine the relation between spatial resolution, image noise and administered radiation dose for a multitude of use-cases. These cases include ultra-high resolution and multi-energy acquisitions of mice administered with a prototype bismuth-based contrast agent (nanoPET Pharma, Berlin, Germany) as well as larger animals and actual patients. The clinical EID provides a spatial resolution of about 9 lp/cm (modulation transfer function at 10%, MTF10%) while UHR allows for the acquisition of images with up to 16 lp/cm allowing for the visualization of all relevant anatomical structures in preclinical and clinical specimen. The spectral capabilities of the system enable a variety of applications previously not available in preclinical research such as pseudo-monochromatic images. Clinical ultra-high resolution photon-counting CT has the potential to unify preclinical and clinical research on a single system enabling versatile imaging of specimens and individuals ranging from mice to man.

Effect of platelet-rich and platelet-poor plasma on 3D bone-to-implant contact: a preclinical micro-CT study

BackgroundBone-to-implant contact ratio (BIC%) plays a critical role in secondary stability of osseointegrated dental implants. The aim of this study was to identify the correlation of 2D/3D micro-CT images with histology as a gold standard for evaluating BIC% and to investigate the influence of the platelet-rich plasma (PRP) and platelet-poor plasma (PPP) on 3D BIC% following delayed implant placement with delayed loading (DIP+DL).MethodsNine beagle dogs were recruited. Following bilateral extraction of mandibular 3rd premolar, 4th premolar, and 1st molar, 54 screw-type titanium implants were inserted and randomly divided into one control and two test groups based on a split-mouth design. The control group involved DIP+DL (n = 18) and both test groups included DIP+DL with local application of PRP (n = 18) and PPP (n = 18). A BIC analysis was performed utilizing 2D histomorphometry and 2D/3D micro-CT. Following identification of correlation between histology and 2D/3D micro-CT images, a 3D micro-CT assessment of the 3D BIC% at three follow-up time-points (1, 3, and 6 months) was carried out for observing the influence of PRP and PPP on BIC.ResultsThe 2D micro-CT BIC% values revealed a strong positive correlation with histology (r = 0.98, p < 0.001) and a moderate correlation existed with 3D micro-CT (r = 0. 67, p = 0.005). BIC levels at 1 month and combined influence of PPP and PRP irrespective of time-points revealed significantly higher 3D BIC% compared to the control. However, a reduction in 3D BIC% was observed at the 3rd and 6th month. No significant difference was observed between both PRP and PPP.ConclusionsBoth 2D and 3D micro-CT demonstrated a potential to be utilized as a complimentary method for assessing BIC compared to the histological gold standard. Overall, both PRP and PPP significantly facilitated bone healing and osseointegration with a higher 3D BIC at follow-up. However, their influence was reduced as the observation period was increased.

Dual source hybrid spectral micro-CT using an energy-integrating and a photon-counting detector

Preclinical micro-CT provides a hotbed in which to develop new imaging technologies, including spectral CT using photon counting detector (PCD) technology. Spectral imaging using PCDs promises to expand x-ray CT as a functional imaging modality, capable of molecular imaging, while maintaining CT’s role as a powerful anatomical imaging modality. However, the utility of PCDs suffers due to distorted spectral measurements, affecting the accuracy of material decomposition. We attempt to improve material decomposition accuracy using our novel hybrid dual-source micro-CT system which combines a PCD and an energy integrating detector. Comparisons are made between PCD-only and hybrid CT results, both reconstructed with our iterative, multi-channel algorithm based on the split Bregman method and regularized with rank-sparse kernel regression. Multi-material decomposition is performed post-reconstruction for separation of iodine (I), gold (Au), gadolinium (Gd), and calcium (Ca). System performance is evaluated first in simulations, then in micro-CT phantoms, and finally in an in vivo experiment with a genetically modified p53fl/fl mouse cancer model with Au, Gd, and I nanoparticle (NP)-based contrasts agents. Our results show that the PCD-only and hybrid CT reconstructions offered very similar spatial resolution at 10% MTF (PCD: 3.50 lp mm−1; hybrid: 3.47 lp mm−1) and noise characteristics given by the noise power spectrum. For material decomposition we note successful separation of the four basis materials. We found that hybrid reconstruction reduces RMSE by an average of 37% across all material maps when compared to PCD-only of similar dose but does not provide much difference in terms of concentration accuracy. The in vivo results show separation of targeted Au and accumulated Gd NPs in the tumor from intravascular iodine NPs and bone. Hybrid spectral micro-CT can benefit nanotechnology and cancer research by providing quantitative imaging to test and optimize various NPs for diagnostic and therapeutic applications.

Performance Evaluation of a Novel Preclinical Micro-CT System In Vitro and In Vivo

With the advent of innovation in the preclinical studies, micro-CT provides optimized resolution by high-power X-ray output tube and flat-panel detector with ultra-short scanning time. The aim of this study was to evaluate the performance of a novel preclinical micro-CT with different parameters and protocols. Imaging quality was evaluated by micro-CT HA and wire phantom. The high power output X-ray tube provides tube voltage from 40 to 90 kV with tube current, 10 to 800 μA. The detector with 1536 × 1944 pixels was implemented by three different binning modes (1 × 1, 2 × 2 and 4 × 4). The GPU-based reconstruction was applied with Feldkamp’s algorithm. The maximum reconstruction volume was 1944 × 1944 × 4536 per scan. The phantom images were acquired by four modes with pixel sizes of 44.9, 22.5,15 and 9 μm. In the animal study, ovariectomy mice were imaged followed by analysis of bone mineral density (BMD) and BV/TV ratio (bone volume/total bone volume). Linearity (R2) measured in all imaging settings were > 0.9 and was 0.99962 at setting of 0.2 mm Cu filter, 90 kV tube voltage and 556 μA tube current. The spatial resolution as measured by full width half-maximum amplitude (FWHM) was 24 µm in the mode ultra-high resolution. The bone analysis results show the operated cohort has high significant (p < 0.05), whereas the control cohort revealed insignificant either in the BMD. In summary, this novel micro-CT system demonstrated the flexible capability and high spatial resolution with ultra-short acquisition time, and a feasible quantitative BMD software.

A Preliminary Investigation into the Use of Edge Illumination X-ray Phase Contrast Micro-CT for Preclinical Imaging

PurposeTo enable a preliminary assessment of the suitability of edge illumination (EI) x-ray phase contrast (XPC) micro x-ray computed tomography (micro-CT) to preclinical imaging. Specifically, to understand how different acquisition schemes and their combination with dedicated data processing affect contrast-to-noise ratio (CNR) and spatial resolution, while providing control over scan time and radiation dose delivery.ProceduresDeceased mice (n = 3) were scanned with an EI XPC micro-CT setup operated under different settings, leading to scan times between 18 h and 13 min. For the shortest scan, the entrance dose was measured with a calibrated PTW 23344 ion chamber. Different data processing methods were applied, retrieving either separate attenuation and phase images, or hybrid (combined attenuation and phase) images. A quantitative comparison was performed based on CNR and spatial resolution measurements for a soft tissue interface.ResultsAll phase-based images have led to a higher CNR for the considered soft tissue interface than the attenuation image, independent of scan time. The best relative CNR (a sixfold increase) was observed in one of the hybrid images. Spatial resolution was found to be connected to scan time, with a resolution of approximately 20 μm and 60 μm achieved for the longest and shortest scans, respectively. An entrance dose of approximately 300 mGy was estimated for the scan performed within 13 min.ConclusionsDespite their preliminary nature, our results suggest that EI XPC bears potential for enhancing the utility of preclinical micro-CT, and, pending further research and development, could ultimately become a valuable technique in this field.

Micro-computed tomography enables rapid surgical margin assessment during breast conserving surgery (BCS): correlation of whole BCS micro-CT readings to final histopathology

BackgroundRoughly 23% of breast conserving surgery (BCS) patients undergo a second re-excision procedure due to pathologically positive surgical margins. We investigated the feasibility and potential value of micro-Computed Tomography (micro-CT) as a surgical margin guidance tool during BCS.MethodsA cohort of 32 BCS specimens was prospectively imaged with a pre-clinical micro-CT system upon arrival in the surgical pathology laboratory. Reconstructed micro-CT scans were evaluated retrospectively by an experienced breast radiologist, who provided binary determinations whether lesions extended to the specimen margin. These readings were then compared to the final pathological diagnosis and to 2D specimen radiography readings.ResultsOf the 32 specimens imaged, 28 had malignant and four had benign pathological diagnoses. Overall five (four malignant, one benign) of the 32 specimens had lesion tissue extending to the margin. For all 32 specimens, micro-CT reconstructions were calculated (< 4 min. acquisition + reconstruction time) and each specimen was volumetrically analyzed by a radiologist. Of the 28 malignant specimen readings, 18 matched the final pathological diagnosis [64%, 95 CI (47%–81%)], with a negative predictive value of 89% [95 CI (74%–96%)]. Micro-CT readings revealed changes in the tumor location and margin status as compared to single-projection radiography readings.ConclusionsMicro-CT scanning of BCS specimens enabled margin status assessment over the entirety of the surgical surface in a clinically relevant time frame, provided additional spatial information over single-projection radiography, and may be a potentially useful BCS guidance tool.

Small, Long Blood Half-Life Iodine Nanoparticle for Vascular and Tumor Imaging

Standard clinical X-ray contrast agents are small iodine-containing molecules that are rapidly cleared by the kidneys and provide robust imaging for only a few seconds, thereby limiting more extensive vascular and tissue biodistribution imaging as well as optimal tumor uptake. They are also not generally useful for preclinical microCT imaging where longer scan times are required for high resolution image acquisition. We here describe a new iodine nanoparticle contrast agent that has a unique combination of properties: 20 nm hydrodynamic diameter, covalent PEG coating, 40 hour blood half-life, 50% liver clearance after six months, accumulation in tumors, and well-tolerated to at least 4 g iodine/kg body weight after intravenous administration in mice. These characteristics are unique among the other iodine nanoparticles that have been previously reported and provide extended-time high contrast vascular imaging and tumor loading. As such, it is useful for preclinical MicroCT animal studies. Potential human applications might include X-ray radiation dose enhancement for cancer therapy and vascular imaging for life-threatening situations where high levels of contrast are needed for extended periods of time.

Low-dose 4D cardiac imaging in small animals using dual source micro-CT

Micro-CT is widely used in preclinical studies, generating substantial interest in extending its capabilities in functional imaging applications such as blood perfusion and cardiac function. However, imaging cardiac structure and function in mice is challenging due to their small size and rapid heart rate. To overcome these challenges, we propose and compare improvements on two strategies for cardiac gating in dual-source, preclinical micro-CT: fast prospective gating (PG) and uncorrelated retrospective gating (RG). These sampling strategies combined with a sophisticated iterative image reconstruction algorithm provide faster acquisitions and high image quality in low-dose 4D (i.e. 3D + Time) cardiac micro-CT. Fast PG is performed under continuous subject rotation which results in interleaved projection angles between cardiac phases. Thus, fast PG provides a well-sampled temporal average image for use as a prior in iterative reconstruction. Uncorrelated RG incorporates random delays during sampling to prevent correlations between heart rate and sampling rate. We have performed both simulations and animal studies to validate these new sampling protocols. Sampling times for 1000 projections using fast PG and RG were 2 and 3 min, respectively, and the total dose was 170 mGy each. Reconstructions were performed using a 4D iterative reconstruction technique based on the split Bregman method. To examine undersampling robustness, subsets of 500 and 250 projections were also used for reconstruction. Both sampling strategies in conjunction with our iterative reconstruction method are capable of resolving cardiac phases and provide high image quality. In general, for equal numbers of projections, fast PG shows fewer errors than RG and is more robust to undersampling. Our results indicate that only 1000-projection based reconstruction with fast PG satisfies a 5% error criterion in left ventricular volume estimation. These methods promise low-dose imaging with a wide range of preclinical applications in cardiac imaging.

Micro-computed tomography–based highly automated 3D segmentation of the rat spine for quantitative analysis of metastatic disease

Noninvasive evaluation of metastatic disease in the spine has generally been limited to 2D qualitative or semiquantitative analysis techniques. This study aims to develop and evaluate a highly automated micro-CT-based quantitative analysis tool that can measure the architectural impact of metastatic involvement in whole vertebrae. Micro-CT analysis of rat whole vertebrae was conducted using a combination of demons deformable registration, level set curvature evolution, and intensity based thresholding techniques along with upsampling and edge enhancement techniques. The algorithm was applied to 6 lumbar vertebrae (L1-3) from 6 rnu/rnu rats (3 healthy rats and 3 with metastatic involvement). Osteolytic metastatic involvement was modeled via MT1 human breast cancer cells. Excellent volumetric concurrency was achieved in comparing the automated micro-CT-based segmentations of the whole vertebrae, trabecular centrums, and individual trabecular networks to manual segmentations (98.9%, 96.1%, and 98.3%, respectively; 6 specimens), and the automated segmentations were achieved in a fraction of the time. The algorithm successfully accounted for discontinuities in the cortical shell caused by vasculature and osteolytic destruction. As such, this work demonstrates the potential of this highly automated segmentation tool to permit rapid precise quantitative structural analysis of the spine with minimum user interaction in the analysis of both healthy and pathological (metastatically involved) vertebrae. Future optimization and the incorporation of lower-resolution imaging parameters may allow automated analysis of clinical CT-based measures in addition to preclinical micro-CT-based analyses of the structural impact and progression of pathological processes in the spine.

Dual-energy attenuation coefficient decomposition with differential filtration and application to a microCT scanner

Dual-energy x-ray computed tomography (DECT) has the capability to decompose attenuation coefficients using two basis functions and has proved its potential in reducing beam-hardening artifacts from reconstructed images. The method typically involves two successive scans with different x-ray tube voltage settings. This work proposes an approach to dual-energy imaging through x-ray beam filtration that requires only one scan and a single tube voltage setting. It has been implemented in a preclinical microCT tomograph with minor modifications. Retrofitting of the microCT scanner involved the addition of an automated filter wheel and modifications to the acquisition and reconstruction software. Results show that beam-hardening artifacts are reduced to noise level. Acquisition of a μ-Compton image is well suited for attenuation-correction of PET images while dynamic energy selection (4D viewing) offers flexibility in image viewing by adjusting contrast and noise levels to suit the task at hand. All dual-energy and single energy reference scans were acquired at the same soft tissue dose level of 50 mGy.