Four-dimensional computed tomography of the left ventricle, Part I: Motion artifact reduction.

PURPOSE: Standard four-dimensional computed tomography (4DCT) cardiac reconstructions typically include spiraling artifacts that depend not only on the motion of the heart but also on the gantry angle range over which the data was acquired. We seek to reduce these motion artifacts and, thereby, improve the accuracy of left ventricular wall positions in 4DCT image series. METHODS: We use a motion artifact reduction approach (ResyncCT) that is based largely on conjugate pairs of partial angle reconstruction (PAR) images. After identifying the key locations where motion artifacts exist in the uncorrected images, paired subvolumes within the PAR images are analyzed with a modified cross-correlation function in order to estimate 3D velocity and acceleration vectors at these locations. A subsequent motion compensation process (also based on PAR images) includes the creation of a dense motion field, followed by a backproject-and-warp style compensation. The algorithm was tested on a 3D printed phantom, which represents the left ventricle (LV) and on challenging clinical cases corrupted by severe artifacts. RESULTS: The results from our preliminary phantom test as well as from clinical cardiac scans show crisp endocardial edges and resolved double-wall artifacts. When viewed as a temporal series, the corrected images exhibit a much smoother motion of the LV endocardial boundary as compared to the uncorrected images. In addition, quantitative results from our phantom studies show that ResyncCT processing reduces endocardial surface distance errors from 0.9 ± 0.8 to 0.2 ± 0.1 mm. CONCLUSIONS: The ResyncCT algorithm was shown to be effective in reducing motion artifacts and restoring accurate wall positions. Some perspectives on the use of conjugate-PAR images and on techniques for CT motion artifact reduction more generally are also given.

A two-dimensional feasibility study of deep learning-based feature detection and characterization directly from CT sinograms.

Machine Learning, especially deep learning, has been used in typical x-ray computed tomography (CT) applications, including image reconstruction, image enhancement, image domain feature detection and image domain feature characterization. To our knowledge, this is the first study on machine learning for feature detection and analysis directly based on CT projection data. Specifically, we present neural network methods for blood vessel detection and characterization in the sinogram domain avoiding any partial volume, beam hardening, or motion artifacts introduced during reconstruction. First, we estimate sinogram domain vessel maps using a residual encoder-decoder convolutional neural network (REDCNN). Next, we estimate the vessel centerline and we extract the vessel-only sinogram from the original sinogram, eliminating any background information. Finally, we use a fully connected neural network to estimate the vessel lumen cross-sectional area from the vessel-only sinogram. We trained and tested the proposed methods using CatSim simulations, real CT measurements of vessel phantoms, and clinical data from the NIH CT image database. We achieved encouraging initial results showing the feasibility of CT analysis in the sinogram domain. In principle, sinogram domain analysis should be possible for many other and more complicated clinical CT analysis tasks. Further studies are needed for this sinogram domain analysis approach to become practical for clinical applications.

Image quality of microcalcifications in digital breast tomosynthesis: effects of projection-view distributions.

PURPOSE: To analyze the effects of projection-view (PV) distribution on the contrast and spatial blurring of microcalcifications on the tomosynthesized slices (X-Y plane) and along the depth (Z) direction for the same radiation dose in digital breast tomosynthesis (DBT). METHODS: A GE GEN2 prototype DBT system was used for acquisition of DBT scans. The system acquires PV images from 21 angles in 3° increments over a ±30° range. From these acquired PV images, the authors selected six subsets of PV images to simulate DBT of different angular ranges and angular increments. The number of PV images in each subset was fixed at 11 to simulate a constant total dose. These different PV distributions were subjectively divided into three categories: uniform group, nonuniform central group, and nonuniform extreme group with different angular ranges and angular increments. The simultaneous algebraic reconstruction technique (SART) was applied to each subset to reconstruct the DBT slices. A selective diffusion regularization method was employed to suppress noise. The image quality of microcalcifications in the reconstructed DBTs with different PV distributions was compared using the DBT scans of an American College of Radiology phantom and three human subjects. The contrast-to-noise ratio (CNR) and the full width at half maximum (FWHM) of the line profiles of microcalcifications within their in-focus DBT slices (parallel to detector plane) and the FWHMs of the interplane artifact spread function (ASF) in the Z-direction (perpendicular to detector plane) were used as image quality measures. RESULTS: The results indicate that DBT acquired with a large angular range or, for an equal angular range,with a large fraction of PVs at large angles yielded superior ASF with smaller FWHM in the Z-direction. PV distributions with a narrow angular range or a large fraction of PVs at small angles had stronger interplane artifacts. In the X-Y focal planes, the effect of PV distributions on spatial blurring depended on the directions. In the X-direction (perpendicular to the chestwall), the normalized line profiles of the calcifications reconstructed with the different PV distributions were similar in terms of FWHM; the differences in the FWHMs between the different PV distributions were less than half a pixel. In the Y-direction (x-ray source motion), the normalized line profiles of the calcifications reconstructed with PVs acquired with a narrow angular range or a large fraction of PVs at small angles had smaller FWHMs and thus less blurring of the line profiles. In addition, PV distributions with a narrow angular range or a large fraction of PVs at small angles yielded slightly higher CNR than those with a wide angular range for small, subtle microcalcifications; however, PV distributions had no obvious effect on CNR for relatively large microcalcifications. CONCLUSIONS: PV distributions affect the image quality of DBT. The relative importance of the impact depends on the characteristics of the signal and the direction (perpendicular or parallel) relative to the direction of x-ray source motion. For a given number of PVs, the angular range and the distribution of the PVs affect the degree of in-plane and interplane blurring in opposite ways. The design of the scan parameters of tomosynthesis systems would require proper consideration of the characteristics of the signals of interest and the potential trade-off of the image quality of different types of signals.

Computer-assisted scan protocol and reconstruction (CASPAR)-reduction of image noise and patient dose.

X-ray computed tomography is a powerful medical imaging device. It allows high-resolution 3-D visualization of the human body. However, one drawback is the health risk associated with ionizing radiation. Simply downscaling the radiation intensities over the entire scan results in increased quantum noise. This paper proposes the concept of computer-assisted scan protocol and reconstruction. More specifically, we propose a method to compute patient and task-specific intensity profiles that achieve an optimal tradeoff between radiation dose and image quality. Therefore, reasonable image variance and dose metrics are derived. Conventional third-generation systems as well as inverted geometry concepts are considered. Two dose/noise minimization problems are formulated and solved by an efficient algorithm providing optimized milliampere (mA)-profiles. Thorax phantom simulations demonstrate the promising advantage of this technique: in this particular example, the dose is reduced by 53% for third-generation systems and by 86% for an inverted geometry in comparison to a sinusoidal mA-profile at a constant upper noise limit.

EFFECTOR OF TRANSCRIPTION2 is involved in xylem differentiation and includes a functional DNA single strand cutting domain.

EFFECTORS OF TRANSCRIPTION2 (ET) are plant-specific regulatory proteins characterized by the presence of two to five C-terminal DNA- and Zn-binding repeats, and a highly conserved cysteine pattern. We describe the structural characterization of the three member Arabidopsis thaliana ET gene family and reveal some allelic sequence polymorphisms. A mutation analysis showed that AtET2 affects the expression of various KNAT genes involved in the maintenance of the undifferentiated state of cambial meristem cells. It also plays a role in the regulation of GA5 (gibberellin 3-beta-dioxygenase) and the cell-cycle-related GASA4. A correlation was established between AtET2 expression and the cellular differentiation state. AtET-GFP fusion proteins shuttle between the cytoplasm and nucleus, with the AtET2 product prevented from entering the nucleus in non-differentiating cells. Within the nucleus, AtET2 probably acts via a single strand cutting domain. A more general regulatory role for ET factors is proposed, governing cell differentiation in cambial meristems, a crucial process for the development of plant vascular tissues.

Optimization of slice sensitivity profile for radiographic tomosynthesis.

Similar to other tomographic imaging modalities, the slice sensitivity profile (SSP) is an important image quality metric for radiographic tomosynthesis. In this study, the relationship between the acquisition angular range (Theta) and the SSP for the linear trajectory system was carefully investigated from both theoretical and experimental perspectives. A mathematical SSP model was derived for arbitrary points in the reconstructed volume. We used a newly developed flat-panel tomosynthesis prototype system to experimentally validate the mathematical model from 20 degrees (+/-10 degrees) to 60 degrees (+/-30 degrees) angular ranges. The SSP was measured by imaging an edge phantom placed at an angle with respect to the detector plane using the modulation transfer function degradation (MTF-d) method. In addition to the experiments, computer simulations were performed to investigate the relationship in a wider angular range (2.5 degrees to 60 degrees). Furthermore, image data from an anthropomorphic phantom were collected to corroborate the system analysis. All the images in this study were constructed using a 3D view-weighted cone-beam filtered backprojection algorithm (3D VW CB-FBP). The theoretical analysis reveals that the SSP of linear trajectory tomosynthesis is inversely proportional to tan(Theta/2). This theory was supported by both simulation (chi2=1.415, DF=7, p =0.985) and phantom experiment (r=0.999, p < 0.001) and was further confirmed by an analysis of the reconstructed images of an anthropomorphic phantom. The results imply that the benefit of narrower SSP by increasing angular range quickly diminishes once beyond 40 degrees. The advantages of the MTF-d method were also demonstrated.

Antisense inhibition of the plastidial glucose-6-phosphate/phosphate translocator in Vicia seeds shifts cellular differentiation and promotes protein storage.

The glucose-6-phosphate/phosphate translocator (GPT) acts as an importer of carbon into the plastid. Despite the potential importance of GPT for storage in crop seeds, its regulatory role in biosynthetic pathways that are active during seed development is poorly understood. We have isolated GPT1 from Vicia narbonensis and studied its role in seed development using a transgenic approach based on the seed-specific legumin promoter LeB4. GPT1 is highly expressed in vegetative sink tissues, flowers and young seeds. In the embryo, localized upregulation of GPT1 at the onset of storage coincides with the onset of starch accumulation. Embryos of transgenic plants expressing antisense GPT1 showed a significant reduction (up to 55%) in the specific transport rate of glucose-6-phosphate as determined using proteoliposomes prepared from embryos. Furthermore, amyloplasts developed later and were smaller in size, while the expression of genes encoding plastid-specific translocators and proteins involved in starch biosynthesis was decreased. Metabolite analysis and stable isotope labelling demonstrated that starch biosynthesis was also reduced, although storage protein biosynthesis increased. This metabolic shift was characterized by upregulation of genes related to nitrogen uptake and protein storage, morphological variation of the protein-storing vacuoles, and a crude protein content of mature seeds of transgenics that was up to 30% higher than in wild-type. These findings provide evidence that (1) the prevailing level of GPT1 abundance/activity is rate-limiting for the synthesis of starch in developing seeds, (2) GPT1 exerts a controlling function on assimilate partitioning into storage protein, and (3) GPT1 is essential for the differentiation of embryonic plastids and seed maturation.

Gradients of lipid storage, photosynthesis and plastid differentiation in developing soybean seeds.

This study establishes a topographical framework for functional investigations on the regulation of lipid biosynthesis and its interaction with embryo photosynthesis in developing soybean seed. Structural observations, combined with molecular and functional parameters, revealed the gradual transformation of chloroplasts into storage organelles, starting from inner regions going outwards. This is evidenced by electron microscopy, confocal laser scanning microscopy, in situ hybridization and histochemical/biochemical data. As a consequence of plastid differentiation, photosynthesis becomes distributed along a gradient within the developing embryo. Electron transport rate, effective quantum yield and O2 production rate are maximal in the embryo periphery, as documented by imaging pulse-amplitude-modulated fluorescence and O2 release via microsensors. The gradual loss of photosynthetic capacity was accompanied by a similarly gradual accumulation of starch and lipids. Noninvasive nuclear magnetic resonance spectroscopy of mature seeds revealed steep gradients in lipid deposition, with the highest concentrations in inner regions. The inverse relationship between photosynthesis and lipid biosynthesis argues against a direct metabolic involvement of photosynthesis in lipid biosynthesis during the late storage stage, but points to a role for photosynthetic oxygen release. This hypothesis is verified in a companion paper.