B Fahimian

Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy

Microscopy has greatly advanced our understanding of biology. Although significant progress has recently been made in optical microscopy to break the diffraction-limit barrier, reliance of such techniques on fluorescent labeling technologies prohibits quantitative 3D imaging of the entire contents of cells. Cryoelectron microscopy can image pleomorphic structures at a resolution of 3–5 nm, but is only applicable to thin or sectioned specimens. Here, we report quantitative 3D imaging of a whole, unstained cell at a resolution of 50–60 nm by X-ray diffraction microscopy. We identified the 3D morphology and structure of cellular organelles including cell wall, vacuole, endoplasmic reticulum, mitochondria, granules, nucleus, and nucleolus inside a yeast spore cell. Furthermore, we observed a 3D structure protruding from the reconstructed yeast spore, suggesting the spore germination process. Using cryogenic technologies, a 3D resolution of 5–10 nm should be achievable by X-ray diffraction microscopy. This work hence paves a way for quantitative 3D imaging of a wide range of biological specimens at nanometer-scale resolutions that are too thick for electron microscopy.

Three-dimensional structure determination from a single view

The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning ‘curved’ and graphein meaning ‘writing’), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 Å resolution, and a single poliovirus at 2–3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.

Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography

Electron tomography is currently the highest resolution imaging modality available to study the 3D structures of pleomorphic macromolecular assemblies, viruses, organelles and cells. Unfortunately, the resolution is currently limited to 3-5nm by several factors including the dose tolerance of biological specimens and the inaccessibility of certain tilt angles. Here we report the first experimental demonstration of equally-sloped tomography (EST) to alleviate these problems. As a proof of principle, we applied EST to reconstructing frozen-hydrated keyhole limpet hemocyanin molecules from a tilt-series taken with constant slope increments. In comparison with weighted back-projection (WBP), the algebraic reconstruction technique (ART) and the simultaneous algebraic reconstruction technique (SART), EST reconstructions exhibited higher contrast, less peripheral noise, more easily detectable molecular boundaries and reduced missing wedge effects. More importantly, EST reconstructions including only two-thirds the original images appeared to have the same resolution as full WBP reconstructions, suggesting that EST can either reduce the dose required to reach a given resolution or allow higher resolutions to be achieved with a given dose. EST was also applied to reconstructing a frozen-hydrated bacterial cell from a tilt-series taken with constant angular increments. The results confirmed similar benefits when standard tilts are utilized.

Low-dose x-ray phase-contrast and absorption CT using equally sloped tomography

Tomographic reconstruction from undersampled and noisy projections is often desirable in transmission CT modalities for purposes of low-dose tomography and fast acquisition imaging. However under such conditions, due to the violation of the Nyquist sampling criteria and the presence of noise, reconstructions with acceptable accuracy may not be possible. Recent experiments in transmission electron tomography and coherent diffraction microscopy have shown that the technique of equally sloped tomography (EST), an exact tomographic method utilizing an oversampling iterative Fourier-based reconstruction, provides more accurate image reconstructions when the number of projections is significantly undersampled relative to filtered back projection and algebraic iterative methods. Here we extend this technique by developing new reconstruction algorithms which allow for the incorporation of advanced mathematical regularization constraints, such as the nonlocal means total variational model, in a manner that is consistent with experimental projections. We then evaluate the resulting image quality of the developed algorithm through simulations and experiments at the European Synchrotron Radiation Facility on image quality phantoms using the x-ray absorption and phase contrast CT modalities. Both our simulation and experimental results have indicated that the method can reduce the number of projections by 60-75% in parallel beam modalities, while achieving comparable or better image quality than the conventional reconstructions. As large-scale and compact synchrotron radiation facilities are currently under rapid development worldwide, the implementation of low-dose x-ray absorption and phase-contrast CT can find broad applications in biology and medicine using these advanced x-ray sources.

Scatter correction in cone‐beam CT via a half beam blocker technique allowing simultaneous acquisition of scatter and image information

PURPOSE X-ray scatter incurred to detectors degrades the quality of cone-beam computed tomography (CBCT) and represents a problem in volumetric image guided and adaptive radiation therapy. Several methods using a beam blocker for the estimation and subtraction of scatter have been proposed. However, due to missing information resulting from the obstruction of the blocker, such methods require dual scanning or dynamically moving blocker to obtain a complete volumetric image. Here, we propose a half beam blocker-based approach, in conjunction with a total variation (TV) regularized Feldkamp-Davis-Kress (FDK) algorithm, to correct scatter-induced artifacts by simultaneously acquiring image and scatter information from a single-rotation CBCT scan. METHODS A half beam blocker, comprising lead strips, is used to simultaneously acquire image data on one side of the projection data and scatter data on the other half side. One-dimensional cubic B-Spline interpolation/extrapolation is applied to derive patient specific scatter information by using the scatter distributions on strips. The estimated scatter is subtracted from the projection image acquired at the opposite view. With scatter-corrected projections where this subtraction is completed, the FDK algorithm based on a cosine weighting function is performed to reconstruct CBCT volume. To suppress the noise in the reconstructed CBCT images produced by geometric errors between two opposed projections and interpolated scatter information, total variation regularization is applied by a minimization using a steepest gradient descent optimization method. The experimental studies using Catphan504 and anthropomorphic phantoms were carried out to evaluate the performance of the proposed scheme. RESULTS The scatter-induced shading artifacts were markedly suppressed in CBCT using the proposed scheme. Compared with CBCT without a blocker, the nonuniformity value was reduced from 39.3% to 3.1%. The root mean square error relative to values inside the regions of interest selected from a benchmark scatter free image was reduced from 50 to 11.3. The TV regularization also led to a better contrast-to-noise ratio. CONCLUSIONS An asymmetric half beam blocker-based FDK acquisition and reconstruction technique has been established. The proposed scheme enables simultaneous detection of patient specific scatter and complete volumetric CBCT reconstruction without additional requirements such as prior images, dual scans, or moving strips.

Development and Optimization of Regularized Tomographic Reconstruction Algorithms Utilizing Equally-Sloped Tomography

We develop two new algorithms for tomographic reconstruction which incorporate the technique of equally-sloped tomography (EST) and allow for the optimized and flexible implementation of regularization schemes, such as total variation constraints, and the incorporation of arbitrary physical constraints. The founding structure of the developed algorithms is EST, a technique of tomographic acquisition and reconstruction first proposed by Miao in 2005 for performing tomographic image reconstructions from a limited number of noisy projections in an accurate manner by avoiding direct interpolations. EST has recently been successfully applied to coherent diffraction microscopy, electron microscopy, and computed tomography for image enhancement and radiation dose reduction. However, the bottleneck of EST lies in its slow speed due to its higher computation requirements. In this paper, we formulate the EST approach as a constrained problem and subsequently transform it into a series of linear problems, which can be accurately solved by the operator splitting method. Based on these mathematical formulations, we develop two iterative algorithms for tomographic image reconstructions through EST, which incorporate Bregman and continuative regularization. Our numerical experiment results indicate that the new tomographic image reconstruction algorithms not only significantly reduce the computational time, but also improve the image quality. We anticipate that EST coupled with the novel iterative algorithms will find broad applications in X-ray tomography, electron microscopy, coherent diffraction microscopy, and other tomography fields.

Trajectory modulated prone breast irradiation: A LINAC-based technique combining intensity modulated delivery and motion of the couch

PURPOSE External beam radiation therapy (EBRT) provides a non-invasive treatment alternative for accelerated partial breast irradiation (APBI), however, limitations in achievable dose conformity of current EBRT techniques have been correlated to reported toxicity. To enhance the conformity of EBRT APBI, a technique for conventional LINACs is developed, which through combined motion of the couch, intensity modulated delivery, and a prone breast setup, enables wide-angular coronal arc irradiation of the ipsilateral breast without irradiating through the thorax and contralateral breast. METHODS AND MATERIALS A couch trajectory optimization technique was developed to determine the trajectories that concurrently avoid collision with the LINAC and maintain the target within the MLC apertures. Inverse treatment planning was performed along the derived trajectory. The technique was experimentally implemented by programming the Varian TrueBeam™ STx in Developer Mode. The dosimetric accuracy of the delivery was evaluated by ion chamber and film measurements in phantom. RESULTS The resulting optimized trajectory was shown to be necessarily non-isocentric, and contain both translation and rotations of the couch. Film measurements resulted in 93% of the points in the measured two-dimensional dose maps passing the 3%/3mm Gamma criterion. Preliminary treatment plan comparison to 5-field 3D-conformal, IMRT, and VMAT demonstrated enhancement in conformity, and reduction of the normal tissue V50% and V100% parameters that have been correlated with EBRT toxicity. CONCLUSIONS The feasibility of wide-angular intensity modulated partial breast irradiation using motion of the couch has been demonstrated experimentally on a standard LINAC for the first time. For patients eligible for a prone setup, the technique may enable improvement of dose conformity and associated dose-volume parameters correlated with toxicity.

Radiation dose reduction in medical x‐ray CT via Fourier‐based iterative reconstruction

PURPOSE A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. METHODS EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. RESULTS Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. CONCLUSIONS A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.

Seeing the invisible: Direct visualization of therapeutic radiation beams using air scintillation

PURPOSE To assess whether air scintillation produced during standard radiation treatments can be visualized and used to monitor a beam in a nonperturbing manner. METHODS Air scintillation is caused by the excitation of nitrogen gas by ionizing radiation. This weak emission occurs predominantly in the 300-430 nm range. An electron-multiplication charge-coupled device camera, outfitted with an f/0.95 lens, was used to capture air scintillation produced by kilovoltage photon beams and megavoltage electron beams used in radiation therapy. The treatment rooms were prepared to block background light and a short-pass filter was utilized to block light above 440 nm. RESULTS Air scintillation from an orthovoltage unit (50 kVp, 30 mA) was visualized with a relatively short exposure time (10 s) and showed an inverse falloff (r(2) = 0.89). Electron beams were also imaged. For a fixed exposure time (100 s), air scintillation was proportional to dose rate (r(2) = 0.9998). As energy increased, the divergence of the electron beam decreased and the penumbra improved. By irradiating a transparent phantom, the authors also showed that Cherenkov luminescence did not interfere with the detection of air scintillation. In a final illustration of the capabilities of this new technique, the authors visualized air scintillation produced during a total skin irradiation treatment. CONCLUSIONS Air scintillation can be measured to monitor a radiation beam in an inexpensive and nonperturbing manner. This physical phenomenon could be useful for dosimetry of therapeutic radiation beams or for online detection of gross errors during fractionated treatments.

Stereotactic Ablative Radiotherapy for the Treatment of Refractory Cardiac Ventricular Arrhythmia

A 71-year-old man with coronary artery disease, coronary artery bypass grafting in 2000, baseline ejection fraction of 0.24, and implantation of a single chamber implanted cardioverter defibrillator (ICD) in 2009 for ventricular tachycardia (VT) presented with continuous episodes of nonsustained and sustained VT refractory to sotalol and mexiletine. Despite angioplasty and stent for coronary artery disease, VT continued for 2 years. Medical history included atrial fibrillation and oxygen-dependent chronic obstructive pulmonary disease. Baseline electrocardiogram (ECG) showed atrial fibrillation with a ventricular rate of 82 beats per minute with inferior Q waves and QRS duration of 90 ms. Twelve-lead ECG during VT showed a regular, wide-complex tachycardia at 160 beats per minute (CL 380–400 ms), with a right bundle branch block pattern, superior axis, precordial transition at V3–V4. His ICD log showed numerous VT episodes, with a single morphology seen on intracardiac ventricular electrogram, cycle length 380–411ms. Episodes were nonsustained, pace-terminated, and shock-terminated. As catheter ablation was relatively medically contraindicated, he consented to a Food and Drug Administration and Institutional Review Board–approved compassionate-use protocol of stereotactic arrhythmia radioablation (STAR), noninvasive ablation of VT substrate by stereotactic ablative radiotherapy (SABR) techniques for tumors. STAR therapy was delivered in October, 2012. Baseline echocardiogram showed a dilated left ventricle (LV), ejection fraction of 0.24, with basal inferior aneurysm, and apical and infero-posterior akinesis. Positron emission tomography–computed tomography showed extensive hypometabolic scar in the LV extending between the LV base and the apex, involving the inferior, inferoseptal, and inferolateral walls. A target for STAR was delineated using proprietary visualization and contouring software (CardioPlan™, CyberHeart™, Portola Valley, CA), outlining the target volume corresponding to what would have been the …