4D micro-CT for cardiac and perfusion applications with view under sampling

Abstract

Purpose Micro-CT is currently used to provide anatomical information in preclinical studies. There is however significant interest in obtaining functional measurements on the same systems. We report here novel strategies for 4D Micro-CT with a focus on two applications: i) cardiac imaging based on retrospective gating and ii) pulmonary perfusion using multiple contrast injections/rotations paradigm. Methods A dual source micro-CT system is used for image acquisition with pulsed x-rays exposures (80 kVp, 70mA, 10 ms) and a sampling rate of 20 projections/sec. The cardiac micro-CT protocol involves the use of a liposomal blood pool contrast agent containing 123 mg I/ml delivered via a tail vein catheter in a dose of 0.01 ml/g body weight. Fast scanning of free breathing mice is achieved using retrospective gating. The ECG and respiratory signals are used to sort projections into 10 cardiac phases. The pulmonary perfusion protocol uses a conventional contrast agent (Isovue 370). The total volume of contrast agent is limited to 0.4 ml and is delivered by a micro-injector in 4 injections separated by 2 minute intervals to allow for clearance. Each injection is synchronized with the rotation of the animal, and each of the 4 rotations is started with an angular offset of 22.5° from the starting angle of the previous rotation. Both cardiac and perfusion protocols result in an irregular angular distribution of projections that causes significant streaking artifacts in reconstructions when using traditional filtered back projection algorithms. To alleviate these artifacts, we construct the point spread function (PSF) of our micro-CT system and analyze the distribution of the reconstructed data in the Fourier domain. This enables us to correct for irregular angular inconsistencies via deconvolution and also identify regions where data is missing. These regions are filled in with data from a high quality but temporally averaged image reconstructed with all available projections. We implemented parts of this algorithm on a graphics processing unit (GPU) to reduce run time. The proposed method was validated with numerical simulations and experimental micro-CT data. Results The simulations indicate that deconvolution successfully removes the streaking artifacts while preserving temporal information. 4D cardiac micro-CT in a mouse was performed with adequate image quality at isotropic voxel size of 88 microns and 10 ms temporal resolution. 4D pulmonary perfusion images were obtained in a mouse at 176 microns and 687 msec temporal resolution. Compared with FBP reconstruction, the streak reduction ratio is 70% and the contrast to noise ratio is 2.5 times greater in the deconvolved images. The radiation dose associated with the proposed methods is in the range of a typical micro-CT dose (0.17 Gy for the cardiac study and 0.21 Gy for the perfusion study). Conclusions The low dose 4D micro-CT imaging protocols presented here can be applied in high throughput longitudinal studies in a wide range of applications, including drug...

Medical image processing on the GPU – Past, present and future

“…Tian et al (2011a) combined GPU acceleration with regularization based on temporal non-local means, inspired by the non-local means denoising algorithm (Buades et al, 2005), to take advantage of the temporal correlation between the volumes. Badea et al (2011) used a GPU to accelerate the reconstruction of 4D data from a micro-CT scanner, for cardiac imaging of mice. Similar work was presented by Johnston et al (2012), who also applied fivedimensional bilateral filtering to further suppress noise levels.…”

Deconvolution for limited-view streak artifacts removal: improvements upon an existing approach

“…In order to remove these streak artifacts, several techniques based on deconvolution have been proposed in the 1980's [3], and recently reintroduced by Badea et al in a paper on 4D micro-CT [4]. The current paper is focused on improving upon this method, and is organized as follows: in section II, we demonstrate that a Radon transform followed by a gated FBP is equivalent to a convolution, and highlight the main challenges a streak removal method has to take on.…”

“…The current paper is focused on improving upon this method, and is organized as follows: in section II, we demonstrate that a Radon transform followed by a gated FBP is equivalent to a convolution, and highlight the main challenges a streak removal method has to take on. Section III provides a short description of the method presented in [4], aimed at explaining how it deals with the specific problems highlighted in section II. Section IV contains the proposed improvements.…”

“…Section IV contains the proposed improvements. Section V describes an iterative deconvolution method that could replace the one used in [4]. Section VI compares the results of all the methods we describe, and finally section VII contains a discussion of the results and limitations of the deconvolution approach.…”

Dual-energy micro-CT of the rodent lung

“…Lung imaging in rodents by micro-CT is extremely challenging because sophisticated instruments and imaging methods are required to cope with the demands of higher resolution and physiologic motion (13). Our group has been actively engaged in designing pulmonary gating techniques for micro-CT (4) as well as in developing methods for pulmonary perfusion imaging (5,6). We have also built a dual source micro-CT system (2) that enables not only faster dynamic imaging but also dual-energy micro-CT studies.…”