Monica Abella

Assessment of a New High-Performance Small-Animal X-Ray Tomograph

We have developed a new X-ray cone-beam tomograph for in vivo small-animal imaging using a flat panel detector (CMOS technology with a microcolumnar CsI scintillator plate) and a microfocus X-ray source. The geometrical configuration was designed to achieve a spatial resolution of about 12 lpmm with a field of view appropriate for laboratory rodents. In order to achieve high performance with regard to per-animal screening time and cost, the acquisition software takes advantage of the highest frame rate of the detector and performs on-the-fly corrections on the detector raw data. These corrections include geometrical misalignments, sensor non-uniformities, and defective elements. The resulting image is then converted to attenuation values. We measured detector modulation transfer function (MTF), detector stability, system resolution, quality of the reconstructed tomographic images and radiated dose. The system resolution was measured following the standard test method ASTM E 1695 -95. For image quality evaluation, we assessed signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) as a function of the radiated dose. Dose studies for different imaging protocols were performed by introducing TLD dosimeters in representative organs of euthanized laboratory rats. Noise figure, measured as standard deviation, was 50 HU for a dose of 10 cGy. Effective dose with standard research protocols is below 200 mGy, confirming that the system is appropriate for in vivo imaging. Maximum spatial resolution achieved was better than 50 micron. Our experimental results obtained with image quality phantoms as well as with in-vivo studies show that the proposed configuration based on a CMOS flat panel detector and a small micro-focus X-ray tube leads to a compact design that provides good image quality and low radiated dose, and it could be used as an add-on for existing PET or SPECT scanners.

Design and performance evaluation of a coplanar multimodality scanner for rodent imaging

This work reports on the development and performance evaluation of the VrPET/CT, a new multimodality scanner with coplanar geometry for in vivo rodent imaging. The scanner design is based on a partial-ring PET system and a small-animal CT assembled on a rotatory gantry without axial displacement between the geometric centers of both fields of view (FOV). We report on the PET system performance based on the NEMA NU-4 protocol; the performance characteristics of the CT component are not included herein. The accuracy of inter-modality alignment and the imaging capability of the whole system are also evaluated on phantom and animal studies. Tangential spatial resolution of PET images ranged between 1.56 mm at the center of the FOV and 2.46 at a radial offset of 3.5 cm. The radial resolution varies from 1.48 mm to 1.88 mm, and the axial resolution from 2.34 mm to 3.38 mm for the same positions. The energy resolution was 16.5% on average for the entire system. The absolute coincidence sensitivity is 2.2% for a 100-700 keV energy window with a 3.8 ns coincident window. The scatter fraction values for the same settings were 11.45% for a mouse-sized phantom and 23.26% for a rat-sized phantom. The peak noise equivalent count rates were also evaluated for those phantoms obtaining 70.8 kcps at 0.66 MBq/cc and 31.5 kcps at 0.11 MBq/cc, respectively. The accuracy of inter-modality alignment is below half the PET resolution, and the image quality of biological specimens agrees with measured performance parameters. The assessment presented in this study shows that the VrPET/CT system is a good performance small-animal imager, while the cost derived from a partial ring detection system is substantially reduced as compared with a full-ring PET tomograph.

rPET detectors design and data processing

Small animal PET systems based on rotating planar detectors posses some interesting advantages for high sensitivity, high resolution imaging. We have designed the rPET detectors based on MLS crystals assembled on a 30times30 matrix optically coupled to a flat-panel PS-PMT. Weighted position readout circuits pre-process the 64 signals from the 8times8 anodes matrix, which are digitized using a charge-integrating converter. The amplification electronics, including the trigger output for coincidence detection, and the high voltage supply are integrated in a three PCBs stack that forms the base attached to the back of the PMT. The whole assembly is enclosed in a light tight, lead (Pb) shielded aluminum box. The detectors are mounted on a rotating gantry with more than 180 degrees rotation span. The digitized events are screened and histogramed, and a modified center of gravity algorithm removes from the position calculation those signals with poor signal to noise ratio. Apparent mean crystal size on the 511 keV field-flood images is 0.6 mm, mean peak-to-valley ratio is better than 8, and intrinsic resolution is 1.5 mm at the central row, with the energy window wide open. Sensitivity (CPS) for a pair of these detectors set in coincidence at 160 mm distance is 1%

Software architecture for multi-bed FDK-based reconstruction in X-ray CT scanners

Most small-animal X-ray computed tomography (CT) scanners are based on cone-beam geometry with a flat-panel detector orbiting in a circular trajectory. Image reconstruction in these systems is usually performed by approximate methods based on the algorithm proposed by Feldkamp et al. (FDK). Besides the implementation of the reconstruction algorithm itself, in order to design a real system it is necessary to take into account numerous issues so as to obtain the best quality images from the acquired data. This work presents a comprehensive, novel software architecture for small-animal CT scanners based on cone-beam geometry with circular scanning trajectory. The proposed architecture covers all the steps from the system calibration to the volume reconstruction and conversion into Hounsfield units. It includes an efficient implementation of an FDK-based reconstruction algorithm that takes advantage of system symmetries and allows for parallel reconstruction using a multiprocessor computer. Strategies for calibration and artifact correction are discussed to justify the strategies adopted. New procedures for multi-bed misalignment, beam-hardening, and Housfield units calibration are proposed. Experiments with phantoms and real data showed the suitability of the proposed software architecture for an X-ray small animal CT based on cone-beam geometry.

Accuracy of CT-based attenuation correction in PET/CT bone imaging

We evaluate the accuracy of scaling CT images for attenuation correction of PET data measured for bone. While the standard tri-linear approach has been well tested for soft tissues, the impact of CT-based attenuation correction on the accuracy of tracer uptake in bone has not been reported in detail. We measured the accuracy of attenuation coefficients of bovine femur segments and patient data using a tri-linear method applied to CT images obtained at different kVp settings. Attenuation values at 511 keV obtained with a (68)Ga/(68)Ge transmission scan were used as a reference standard. The impact of inaccurate attenuation images on PET standardized uptake values (SUVs) was then evaluated using simulated emission images and emission images from five patients with elevated levels of FDG uptake in bone at disease sites. The CT-based linear attenuation images of the bovine femur segments underestimated the true values by 2.9 ± 0.3% for cancellous bone regardless of kVp. For compact bone the underestimation ranged from 1.3% at 140 kVp to 14.1% at 80 kVp. In the patient scans at 140 kVp the underestimation was approximately 2% averaged over all bony regions. The sensitivity analysis indicated that errors in PET SUVs in bone are approximately proportional to errors in the estimated attenuation coefficients for the same regions. The variability in SUV bias also increased approximately linearly with the error in linear attenuation coefficients. These results suggest that bias in bone uptake SUVs of PET tracers ranges from 2.4% to 5.9% when using CT scans at 140 and 120 kVp for attenuation correction. Lower kVp scans have the potential for considerably more error in dense bone. This bias is present in any PET tracer with bone uptake but may be clinically insignificant for many imaging tasks. However, errors from CT-based attenuation correction methods should be carefully evaluated if quantitation of tracer uptake in bone is important.

Surfing the optimization space of a multiple-GPU parallel implementation of a X-ray tomography reconstruction algorithm

The increasing popularity of massively parallel architectures based on accelerators have opened up the possibility of significantly improving the performance of X-ray computed tomography (CT) applications towards achieving real-time imaging. However, achieving this goal is a challenging process, as most CT applications have not been designed for exploiting the amount of parallelism existing in these architectures. In this paper we present the massively parallel implementation and optimization of Mangoose++, a CT application for reconstructing 3D volumes from 2D images collected by scanners based on cone-beam geometry. The main contribution of this paper are the following. First, we develop a modular application design that allows to exploit the functional parallelism inside the application and to facilitate the parallelization of individual application phases. Second, we identify a set of optimizations that can be applied individually and in combination for optimally deploying the application on a massively parallel multi-GPU system. Third, we present a study of surfing the optimization space of the modularized application and demonstrate that a significant benefit can be obtained from employing the adequate combination of application optimizations.

A SPECT Scanner for Rodent Imaging Based on Small-Area Gamma Cameras

We developed a cost-effective SPECT scanner prototype (rSPECT) for in vivo imaging of rodents based on small-area gamma cameras. Each detector consists of a position-sensitive photomultiplier tube (PS-PMT) coupled to a 30 x 30 Nal(Tl) scintillator array and electronics attached to the PS-PMT sockets for adapting the detector signals to an in-house developed data acquisition system. The detector components are enclosed in a lead-shielded case with a receptacle to insert the collimators. System performance was assessed using 99mTc for a high-resolution parallel-hole collimator, and for a 0.75-mm pinhole collimator with a 60° aperture angle and a 42-mm collimator length. The energy resolution is about 10.7% of the photopeak energy. The overall system sensitivity is about 3 cps/μCi/detector and planar spatial resolution ranges from 2.4 mm at 1 cm source-to-collimator distance to 4.1 mm at 4.5 cm with parallel-hole collimators. With pinhole collimators planar spatial resolution ranges from 1.2 mm at 1 cm source-to-collimator distance to 2.4 mm at 4.5 cm; sensitivity at these distances ranges from 2.8 to 0.5 cps/μCi/detector. Tomographic hot-rod phantom images are presented together with images of bone, myocardium and brain of living rodents to demonstrate the feasibility of preclinical small-animal studies with the rSPECT.

Co-planar PET/CT for small animal imaging

A small animal PET/CT system based on a common rotating gantry is proposed. The PET detection subsystem is composed of two detector modules based on MLS arrays and four flat panel type PS-PMT. The CT subsystem consists in a micro-focus X-ray tube and a semiconductor X-ray detector. Space for opposed PET detectors and the CT scanner have been allocated on the same plane in such a way that the trans-axial and axial centers are common for both systems. Shielding elements have been placed around the detectors to avoid cross modality contamination. The gantry can rotate 370 degrees to provide complete data sets for the CT image reconstruction algorithm that is based on the cone beam geometry. PET image reconstruction is implemented using FBP (2D and 3D) and OSEM. Sequential acquisition protocols minimize the scan duration, and CT information can be used to implement PET imaging corrections. The coplanar configuration of this system provides intrinsically co-registered data sets, and it is not necessary to reposition the animal to perform any modality imaging, avoiding undesired animal or additional accessories movements. An additional advantage is the compactness of the system that saves space and allows a direct visual monitoring of the animal during the scan.

Design an development of a high performance micro-CT system for small animal imaging

The goal of this work was the development of a low-cost micro-CT scanner, which could be used as an add-on in our previously developed PET systems for small-animals. The scanner design consists of a single-processor computer controlling a micro-focus X-ray tube and a flat panel detector, assembled in a common rotating gantry. The geometrical configuration was selected to achieve a spatial resolution of about 12 lp/mm with a field of view appropriate for small animals such as mice and rats. The radiated dose is controlled during the acquisition by two different elements: an aluminium filter and a tungsten shutter, attached to the X-ray source. The shutter is controlled by the computer in synchronism with the gantry rotation and the detector image integration. In order to achieve high performance with regards to per-animal screening time and cost, the acquisition protocol is able to take advantage from the highest frame rate of the detector also performing on-the-fly corrections for the detector raw data. These corrections include geometrical misalignments, sensor non-uniformities and defective elements, as well as conversion to attenuation images. An FDK reconstruction algorithm adapted to the specific cone-beam geometry has been implemented. Symmetries are exploited to accelerate the algorithm and fast back-projection techniques have been developed for those protocols where high resolution is not a requirement.

Investigation of Different Sparsity Transforms for the PICCS Algorithm in Small-Animal Respiratory Gated CT

Respiratory gating helps to overcome the problem of breathing motion in cardiothoracic small-animal imaging by acquiring multiple images for each projection angle and then assigning projections to different phases. When this approach is used with a dose similar to that of a static acquisition, a low number of noisy projections are available for the reconstruction of each respiratory phase, thus leading to streak artifacts in the reconstructed images. This problem can be alleviated using a prior image constrained compressed sensing (PICCS) algorithm, which enables accurate reconstruction of highly undersampled data when a prior image is available. We compared variants of the PICCS algorithm with different transforms in the prior penalty function: gradient, unitary, and wavelet transform. In all cases the problem was solved using the Split Bregman approach, which is efficient for convex constrained optimization. The algorithms were evaluated using simulations generated from data previously acquired on a micro-CT scanner following a high-dose protocol (four times the dose of a standard static protocol). The resulting data were used to simulate scenarios with different dose levels and numbers of projections. All compressed sensing methods performed very similarly in terms of noise, spatiotemporal resolution, and streak reduction, and filtered back-projection was greatly improved. Nevertheless, the wavelet domain was found to be less prone to patchy cartoon-like artifacts than the commonly used gradient domain.