Keith E. Schubert

A Fast Experimental Scanner for Proton CT: Technical Performance and First Experience With Phantom Scans

We report on the design, fabrication, and first tests of a tomographic scanner developed for proton computed tomography (pCT) of head-sized objects. After extensive preclinical testing, pCT is intended to be employed in support of proton therapy treatment planning and pre-treatment verification in patients undergoing particle-beam therapy. The scanner consists of two silicon-strip telescopes that track individual protons before and after the phantom, and a novel multistage scintillation detector that measures a combination of the residual energy and range of the proton, from which we derive the water equivalent path length (WEPL) of the protons in the scanned object. The set of WEPL values and the associated paths of protons passing through the object over a 360 ° angular scan are processed by an iterative, parallelizable reconstruction algorithm that runs on modern GP-GPU hardware. In order to assess the performance of the scanner, we have performed tests with 200 MeV protons from the synchrotron of the Loma Linda University Medical Center and the IBA cyclotron of the Northwestern Medicine Chicago Proton Center. Our first objective was calibration of the instrument, including tracker channel maps and alignment as well as the WEPL calibration. Then we performed the first CT scans on a series of phantoms. The very high sustained rate of data acquisition, exceeding one million protons per second, allowed a full 360 ° scan to be completed in less than 10 minutes, and reconstruction of a CATPHAN 404 phantom verified accurate reconstruction of the proton relative stopping power in a variety of materials.

Results from a Prototype Proton-CT Head Scanner

Abstract We are exploring low-dose proton radiography and computed tomography (pCT) as techniques to improve the accuracy of proton treatment planning and to provide artifact-free images for verification and adaptive therapy at the time of treatment. Here we report on comprehensive beam test results with our prototype pCT head scanner. The detector system and data acquisition attain a sustained rate of more than a million protons individually measured per second, allowing a full CT scan to be completed in six minutes or less of beam time. In order to assess the performance of the scanner for proton radiography as well as computed tomography, we have performed numerous scans of phantoms at the Northwestern Medicine Chicago Proton Center including a custom phantom designed to assess the spatial resolution, a phantom to assess the measurement of relative stopping power, and a dosimetry phantom. Some images, performance, and dosimetry results from those phantom scans are presented together with a description of the instrument, the data acquisition system, and the calibration methods.

Results from a pre-clinical head scanner for proton CT

We report on the first beam test results with our pre-clinical (Phase-II) head scanner developed for proton computed tomography (pCT). After extensive preclinical testing, pCT will be employed in support of proton therapy treatment planning and pre-treatment verification in patients undergoing treatment with particle beam therapy. The Phase-II pCT system consists of two silicon-strip telescopes that track individual protons before and after the phantom or patient, and a novel multistage scintillation detector that measures a combination of the residual energy and range of the proton, from which we derive the water equivalent path length (WEPL) of the protons in the scanned object. The set of WEPL values and associated paths of protons passing through the object over a 360° angular scan is processed by an iterative, parallelizable reconstruction algorithm that runs on modern GP-GPU hardware. In order to assess the performance of the scanner, we have performed beam tests with 200 MeV protons from the synchrotron of the Loma Linda University Medical Center. The first objective was the calibration of the instrument, including tracker channel maps and alignment as well as the WEPL calibration. Then we performed the first CT scans on a series of phantoms. The very high sustained rate of data acquisition, exceeding one million protons per second, allowed a full 360° scan to be completed in less than 10 minutes, and reconstruction of a CATPHAN 404 phantom verified accurate reconstruction of the proton relative stopping power in a variety of materials.

Application of fluence field modulation to proton computed tomography for proton therapy imaging.

This simulation study presents the application of fluence field modulated computed tomography, initially developed for x-ray CT, to proton computed tomography (pCT). By using pencil beam (PB) scanning, fluence modulated pCT (FMpCT) may achieve variable image quality in a pCT image and imaging dose reduction. Three virtual phantoms, a uniform cylinder and two patients, were studied using Monte Carlo simulations of an ideal list-mode pCT scanner. Regions of interest (ROI) were selected for high image quality and only PBs intercepting them preserved full fluence (FF). Image quality was investigated in terms of accuracy (mean) and noise (standard deviation) of the reconstructed proton relative stopping power compared to reference values. Dose calculation accuracy on FMpCT images was evaluated in terms of dose volume histograms (DVH), range difference (RD) for beam-eye-view (BEV) dose profiles and gamma evaluation. Pseudo FMpCT scans were created from broad beam experimental data acquired with a list-mode pCT prototype. FMpCT noise in ROIs was equivalent to FF images and accuracy better than  -1.3%(-0.7%) by using 1% of FF for the cylinder (patients). Integral imaging dose reduction of 37% and 56% was achieved for the two patients for that level of modulation. Corresponding DVHs from proton dose calculation on FMpCT images agreed to those from reference images and 96% of BEV profiles had RD below 2 mm, compared to only 1% for uniform 1% of FF. Gamma pass rates (2%, 2 mm) were 98% for FMpCT while for uniform 1% of FF they were as low as 59%. Applying FMpCT to preliminary experimental data showed that low noise levels and accuracy could be preserved in a ROI, down to 30% modulation. We have shown, using both virtual and experimental pCT scans, that FMpCT is potentially feasible and may allow a means of imaging dose reduction for a pCT scanner operating in PB scanning mode. This may be of particular importance to proton therapy given the low integral dose found outside the target.

A Model for Entropy of Parallel Execution

In this paper we develop a theory of visualizing a parallel execution by the entropy of the phase space induced by its traces. This metric is then shown to be able to both theoretically and practically find program issues, such as starvation due to data in one of its threads.

Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert

In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439) and genus (p < 0.006) levels, including multiple biochemical and geochemical trends (p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.

Incorporating robustness in diagonally-relaxed orthogonal projections method for proton computed tomography

Iterative algorithms such as ART, DROP, and CARP are commonly used in reconstructing computed tomography images, but only account for errors in the measurements. Errors in the predicted path and intersection lengths, or even blocks of missing measurements can result in degraded image quality. Robust techniques allow for errors in other areas of the model and produce good images that show less sensitivity. In this paper we introduce a robust version of DROP and compare its performance advantages to the standard DROP algorithm on on real data.

Evaluation of Mathematical Algorithms for Automatic Patient Alignment in Radiosurgery

Image registration techniques based on anatomical features can serve to automate patient alignment for intracranial radiosurgery procedures in an effort to improve the accuracy and efficiency of the alignment process as well as potentially eliminate the need for implanted fiducial markers. To explore this option, four two-dimensional (2D) image registration algorithms were analyzed: the phase correlation technique, mutual information (MI) maximization, enhanced correlation coefficient (ECC) maximization, and the iterative closest point (ICP) algorithm. Digitally reconstructed radiographs from the treatment planning computed tomography scan of a human skull were used as the reference images, while orthogonal digital x-ray images taken in the treatment room were used as the captured images to be aligned. The accuracy of aligning the skull with each algorithm was compared to the alignment of the currently practiced procedure, which is based on a manual process of selecting common landmarks, including implanted fiducials and anatomical skull features. Of the four algorithms, three (phase correlation, MI maximization, and ECC maximization) demonstrated clinically adequate (ie, comparable to the standard alignment technique) translational accuracy and improvements in speed compared to the interactive, user-guided technique; however, the ICP algorithm failed to give clinically acceptable results. The results of this work suggest that a combination of different algorithms may provide the best registration results. This research serves as the initial groundwork for the translation of automated, anatomy-based 2D algorithms into a real-world system for 2D-to-2D image registration and alignment for intracranial radiosurgery. This may obviate the need for invasive implantation of fiducial markers into the skull and may improve treatment room efficiency and accuracy.