Investigation of a 2D two-point maximum entropy regularization method for signal-to-noise ratio enhancement: application to CT polymer gel dosimetry

Clinical applicability of Linac-integrated CBCT based NIPAM 3D dosimetry: a dual-institutional investigation

Objective.To develop and benchmark a novel 3D dose verification technique consisting of polymer gel dosimetry (PGD) with cone-beam-CT (CBCT) readout through a two-institution study. The technique has potential for wide and robust applicability through reliance on CBCT readout.Approach. Three treatment plans (3-field, TG119-C-shape spine, 4-target SRS) were created by two independent institutions (Institutions A and B). A Varian Truebeam linear accelerator was used to deliver the plans to NIPAM polymer gel dosimeters produced at both institutions using an identical approach. For readout, a slow CBCT scan mode was used to acquire pre- and post-irradiation images of the gel (1 mm slice thickness). Independent gel analysis tools were used to process the PGD images (A: VistaAce software, B: in-house MATLAB code). Comparing planned and measured doses, the analysis involved a combination of 1D line profiles, 2D contour plots, and 3D global gamma maps (criteria ranging between 2%1 mm and 5%2 mm, with a 10% dose threshold).Main results. For all gamma criteria tested, the 3D gamma pass rates were all above 90% for 3-field and 88% for the SRS plan. For the C-shape spine plan, we benchmarked our 2% 2 mm result against previously published work using film analysis (93.4%). For 2%2 mm, 99.4% (Institution A data), and 89.7% (Institution B data) were obtained based on VistaAce software analysis, 83.7% (Institution A data), and 82.9% (Institution B data) based on MATLAB.Significance. The benchmark data demonstrate that when two institutions follow the same rigorous procedures gamma passing rates up to 99%, for 2%2 mm criteria can be achieved for substantively different treatment plans. The use of different software and calibration techniques may have contributed to the variation in the 3D gamma results. By sharing the data across institutions, we observe the gamma passing rate is more consistent within each pipeline, indicating the need for standardized analysis methods.

Technical Note: Radiotherapy dose characterization of gel dosimetry using shear wave elasticity imaging

PURPOSE

Radiotherapy is an effective treatment for many types of cancer in clinical settings. Gel dosimetry has the potential to record three-dimensional (3D) dose distribution compared to a conventional ion chamber. As the elasticity of the gel is altered after irradiation due to gel polymerization, we aim to measure the dose recorded in gel dosimetry with ultrasonic shear wave elasticity imaging (SWEI), a nondestructive and quantitative elasticity imaging tool.

METHODS

In this study, a cylindrical N-isopropylacrylamide (NIPAM) polymer gel with a diameter of 10 cm and a height of 10 cm and with cellulose as an ultrasonic scatterer was irradiated by a linear accelerator with the irradiation parameters of 6 MV x-ray, dose rate of 100 cGy/min and field size of 10  ×  20 mm² . The six gel phantoms were irradiated with the dose of 0, 1, 3, 5, 8, or 10 Gy. The gel phantoms were measured with SWEI at 24, 36, and 48 h after x-ray irradiation. The two-dimensional (2D) shear wave velocity and Young's modulus maps corresponding to x-ray dose distribution were reconstructed following a time-of-flight reconstruction from a set of time-series displacement maps. The spatial resolution of the reconstructed SWEI image is ~1 mm.

RESULTS

Our results show that the elastic modulus increases linearly as irradiation dose increases (R²  = 0.94 at 24 h, R²  = 0.98 at 36 h, R²  = 0.98 at 48 h), suggesting that the gel elasticity is highly associated with x-ray irradiation dose at 36 h post irradiation, and the dose resolution was 0.66 kPa/Gy. From the 3D elastic modulus maps, the dose distribution along the depth and lateral direction can be reflected in the NIPAM gel dosimetry using SWEI as well.

CONCLUSIONS

In this study, the irradiated NIPAM gel phantom was quantitatively measured with SWEI for the first time to read the dose distribution recorded in the gel dosimetry. The results suggest that the gel elasticity is highly associated with x-ray irradiation dose. In the future, 2D/or 3D dose distribution from intensity modulated radiotherapy (IMRT) or other potential particle radiotherapy will be measured and reconstructed with SWEI and compared with the dose map from a treatment planning system (TPS) in the clinic.

Development and integration of block operations for data invariant automation of digital preprocessing and analysis of biological and biomedical Raman spectra

High-throughput information extraction from large numbers of Raman spectra is becoming an increasingly taxing problem due to the proliferation of new applications enabled using advances in instrumentation. Fortunately, in many of these applications, the entire process can be automated, yielding reproducibly good results with significant time and cost savings. Information extraction consists of two stages, preprocessing and analysis. We focus here on the preprocessing stage, which typically involves several steps, such as calibration, background subtraction, baseline flattening, artifact removal, smoothing, and so on, before the resulting spectra can be further analyzed. Because the results of some of these steps can affect the performance of subsequent ones, attention must be given to the sequencing of steps, the compatibility of these sequences, and the propensity of each step to generate spectral distortions. We outline here important considerations to effect full automation of Raman spectral preprocessing: what is considered full automation; putative general principles to effect full automation; the proper sequencing of processing and analysis steps; conflicts and circularities arising from sequencing; and the need for, and approaches to, preprocessing quality control. These considerations are discussed and illustrated with biological and biomedical examples reflecting both successful and faulty preprocessing.

A matrix-based two-dimensional regularization algorithm for signal-to-noise ratio enhancement of multidimensional spectral data

We present a new spectral image processing algorithm, the "matrix maximum entropy method" (MxMEM), which offers efficient signal-to-noise ratio (SNR) enhancement of multidimensional spectral data. MxMEM is based upon two previous regularization methods that employ the maximum entropy concept. The first is a one-dimensional (1D) algorithm, which smoothes individual vectors, called the two-point maximum entropy method (TPMEM). The second is a two-dimensional (2D) form called 2D TPMEM, that smoothes images but processes them one vector at a time. MxMEM is a truly two dimensional image processing algorithm in that its "smoothing engine" performs two-dimensional processing in every iteration. We demonstrate that this matrix-based construction makes more effective use of two-dimensionally embedded information and thus confers significant advantages over other regularization approaches. In addition, we utilize the concept that individual related Raman spectra can be combined in a matrix to form an artificial Raman "image". We show that, when processed as an image, superior SNR enhancement is achieved compared to processing the same data by TPMEM one spectrum at a time.

Variability in Raman spectra of single human tumor cells cultured in vitro: correlation with cell cycle and culture confluency

In this work we investigate the capability of Raman microscopy (RM) to detect inherent sources of biochemically based spectral variability between single cells of a human tumor cell line (DU145) cultured in vitro. Principal component analysis (PCA) is used to identify differences in single-cell Raman spectra. These spectral differences correlate with (1) cell cycle progression and (2) changing confluency of a cell culture during the first 3 to 4 days after sub-culturing. Cell cycle regulatory drugs are used to synchronize the cell cycle progression of cell cultures, and flow cytometry is used to determine the cell cycle distribution of cell cultures at the time of Raman analysis. Spectral variability arising from cell cycle progression is (1) expressed as varying intensities of protein and nucleic acid features relative to lipid features, (2) well correlated with known biochemical changes in cells as they progress through the cell cycle, and (3) shown to be the most significant source of inherent spectral variability between cells. Furthermore, the specific biomolecules responsible for the observed spectral variability due to both cell cycle progression and changes in cell culture confluency can be identified in the first and second components of principal component analysis (PCA). Our characterization of the inherent sources of variability in Raman spectra of single human cells will be useful for understanding subtle spectral differences in RM studies of single cells.

Polymer gel dosimetry

Polymer gel dosimeters are fabricated from radiation sensitive chemicals which, upon irradiation, polymerize as a function of the absorbed radiation dose. These gel dosimeters, with the capacity to uniquely record the radiation dose distribution in three-dimensions (3D), have specific advantages when compared to one-dimensional dosimeters, such as ion chambers, and two-dimensional dosimeters, such as film. These advantages are particularly significant in dosimetry situations where steep dose gradients exist such as in intensity-modulated radiation therapy (IMRT) and stereotactic radiosurgery. Polymer gel dosimeters also have specific advantages for brachytherapy dosimetry. Potential dosimetry applications include those for low-energy x-rays, high-linear energy transfer (LET) and proton therapy, radionuclide and boron capture neutron therapy dosimetries. These 3D dosimeters are radiologically soft-tissue equivalent with properties that may be modified depending on the application. The 3D radiation dose distribution in polymer gel dosimeters may be imaged using magnetic resonance imaging (MRI), optical-computerized tomography (optical-CT), x-ray CT or ultrasound. The fundamental science underpinning polymer gel dosimetry is reviewed along with the various evaluation techniques. Clinical dosimetry applications of polymer gel dosimetry are also presented.

Polymer gel dosimetry

Polymer gel dosimeters are fabricated from radiation sensitive chemicals which, upon irradiation, polymerize as a function of the absorbed radiation dose. These gel dosimeters, with the capacity to uniquely record the radiation dose distribution in three-dimensions (3D), have specific advantages when compared to one-dimensional dosimeters, such as ion chambers, and two-dimensional dosimeters, such as film. These advantages are particularly significant in dosimetry situations where steep dose gradients exist such as in intensity-modulated radiation therapy (IMRT) and stereotactic radiosurgery. Polymer gel dosimeters also have specific advantages for brachytherapy dosimetry. Potential dosimetry applications include those for low-energy x-rays, high-linear energy transfer (LET) and proton therapy, radionuclide and boron capture neutron therapy dosimetries. These 3D dosimeters are radiologically soft-tissue equivalent with properties that may be modified depending on the application. The 3D radiation dose distribution in polymer gel dosimeters may be imaged using magnetic resonance imaging (MRI), optical-computerized tomography (optical-CT), x-ray CT or ultrasound. The fundamental science underpinning polymer gel dosimetry is reviewed along with the various evaluation techniques. Clinical dosimetry applications of polymer gel dosimetry are also presented.

The use of ultraviolet resonance Raman spectroscopy in the analysis of ionizing-radiation-induced damage in DNA

Ultraviolet resonance Raman spectroscopy (UVRRS) was used to determine damage done in both calf-thymus DNA (CT-DNA) and a short stranded DNA oligomer (SS-DNA) due to ionizing radiation from a medical (60)Co radiation therapy unit used in the treatment of cancer. Spectra were acquired at incident UV wavelengths of 248, 257, and 264 nm in order to utilize the differences in UVRR cross-sections of the bases with wavelength. Through the analysis of difference spectra between irradiated and unirradiated DNA at each of the incident UV wavelengths, damage to CT- and SS-DNA was observed and identified. Significant radiation-induced increases in the difference spectra of the CT-DNA indicated disruption of the stable, stacked structure of its bases, as well as the disruption of Watson-Crick hydrogen bonds between the base pairs. Base unstacking was not as evident in the SS-DNA, while radiation-induced spectral decreases suggest disruption of the structure of the nucleotides. As demonstrated, UVRRS has the ability to highlight contributions from specific moieties with the use of varying incident UV wavelengths, thus enhancing the already information-rich content of the Raman spectra.

Effects of glycerol co-solvent on the rate and form of polymer gel dose response

A factor currently limiting the clinical utility of x-ray CT polymer gel dosimetry is the overall low dose sensitivity (and hence low dose resolution) of the system. Hence, active research remains in the investigation of polymer gel formulations with increased CT dose response. An ideal polymer gel dosimeter will exhibit a sensitive CT response which is linear over a suitable dose range, making clinical implementation reasonably straightforward. This study reports on the variations in rate and form of the CT dose response of irradiated polymer gels manufactured with glycerol, which is a co-solvent that permits dissolution of additional bisacrylamide above its water solubility limit (3% by weight). This study focuses on situations where the concentration of bisacrylamide is kept at or below its water solubility limit so that the influence of the co-solvent on the dose response can be explored separately from the effects of increased cross-linker concentration. CT imaging and Raman spectroscopy are used to construct dose-response curves for irradiated gels varying in (i) initial total monomer (%T) and (ii) initial co-solvent concentration. Results indicate that: (i) for a fixed glycerol concentration, gel response increases linearly with %T. Furthermore, the functional form of the dose response remains constant, in agreement with a previous model of polymer formation. (ii) Polymer gels with constant %T and increasing co-solvent concentrations also show enhanced CT response. In addition, the functional form of the response is altered in these gels as co-solvent concentration is increased. Raman data indicate that the fraction of bis-acrylamide incorporated into polymerization, as opposed to cyclization, increases as co-solvent concentration increases. The changes in functional form indicate varying polymer yields (per unit dose), akin to relative fractional monomer/cross-linker (i.e. %C) changes in earlier studies. These results are put into context of the model of polymer formation. The implications of these results on the clinical utility of polymer gels with co-solvent are highlighted.

Fully automated high-performance signal-to-noise ratio enhancement based on an iterative three-point zero-order Savitzky-Golay filter

The automated processing of data from high-throughput and real-time collection procedures is becoming a pressing problem. Currently the focus is shifting to automated smoothing techniques where, unlike background subtraction techniques, very few methods exist. We have developed a filter based on the widely used and conceptually simple moving average method or zero-order Savitzky-Golay filter and its iterative relative, the Kolmogorov-Zurbenko filter. A crucial difference, however, between these filters and our implementation is that our fully automated smoothing filter requires no parameter specification or parameter optimization. Results are comparable to, or better than, Savitzky-Golay filters with optimized parameters and superior to the automated iterative median filter. Our approach, because it is based on the highly familiar moving average concept, is intuitive, fast, and straightforward to implement and should therefore be of immediate and considerable practical use in a wide variety of spectroscopy applications.

Chi-squared-based filters for high-fidelity signal-to-noise ratio enhancement of spectra

When reconstructing a measured spectrum to enhance its signal-to-noise ratio (SNR), the objective is to minimize the variance between the smooth reconstructed spectrum and the original measured spectrum, hence to attain an acceptably small chi2 value. The chi2 value thus measures the fidelity of the reconstruction to the original. Smoothness can be conceived as attenuated variation between adjacent points in a spectrum. Thus, a conceptual change in the application of the chi2 function to the difference between adjacent points of the reconstructed spectrum permits its use, in principle, as both a measure of smoothness and a measure of fidelity. We show here that implementations of this concept produce results superior to Savitzky-Golay filters.

Adaptive mean filtering for noise reduction in CT polymer gel dosimetry

X-ray computed tomography (CT) as a method of extracting 3D dose information from irradiated polymer gel dosimeters is showing potential as a practical means to implement gel dosimetry in a radiation therapy clinic. However, the response of CT contrast to dose is weak and noise reduction is critical in order to achieve adequate dose resolutions with this method. Phantom design and CT imaging technique have both been shown to decrease image noise. In addition, image postprocessing using noise reduction filtering techniques have been proposed. This work evaluates in detail the use of the adaptive mean filter for reducing noise in CT gel dosimetry. Filter performance is systematically tested using both synthetic patterns mimicking a range of clinical dose distribution features as well as actual clinical dose distributions. Both low and high signal-to-noise ratio (SNR) situations are examined. For all cases, the effects of filter kernel size and the number of iterations are investigated. Results indicate that adaptive mean filtering is a highly effective tool for noise reduction CT gel dosimetry. The optimum filtering strategy depends on characteristics of the dose distributions and image noise level. For low noise images (SNR approximately 20), the filtered results are excellent and use of adaptive mean filtering is recommended as a standard processing tool. For high noise images (SNR approximately 5) adaptive mean filtering can also produce excellent results, but filtering must be approached with more caution as spatial and dose distortions of the original dose distribution can occur.

X-ray CT dose in normoxic polyacrylamide gel dosimetry

This study reports on the effects of x-ray CT dose in CT imaged normoxic polyacrylamide (nPAG) gel dosimeters. The investigation is partitioned into three sections. First, the CT dose absorbed in nPAG is quantified under a range of typical gel CT imaging protocols. It is found that the maximum absorbed CT dose occurs for volumetric imaging and is in the range of 4.6 +/- 0.2 cGy/image. This does scales linearly with image averaging. Second, using Raman spectroscopy, the response of nPAG to CT imaging photon energies (i.e., 120-140 kVp) is established and compared to the well known dose response of nPAG exposed to 6 MV photons. It is found that nPAG exhibits a weaker response (per unit dose) to 140-kVp incident photons as compared to 6 MV incident photons (slopes m6 mv = -0.0374 +/- 0.0006 Gy(-1) and m140 kVp = -0.016 +/- 0.001 Gy(-1)). Finally, using the above data, an induced change in CT number (deltaN(CT)) is calculated for nPAG imaged using a range of gel imaging protocols. It is found that under typical imaging protocols (120-140 kVp, 200 mAs, approximately 16-32 image averages) a deltaN(CT) < 0.2 H is induced in active nPAG dosimeters. This deltaN(CT) is below the current limit of detectability of CT nPAG polymer gel dosimetry. Under expanded imaging protocols (e.g., very high number of image averages) an induced deltaN(CT) of approximately 0.5 H is possible. In these situations the additional polymerization occurring in nPAG due to the imaging process may need to be accounted for.

Characterization of a parallel-beam CCD optical-CT apparatus for 3D radiation dosimetry

3D measurement of optical attenuation is of interest in a variety of fields of biomedical importance, including spectrophotometry, optical projection tomography (OPT) and analysis of 3D radiation dosimeters. Accurate, precise and economical 3D measurements of optical density (OD) are a crucial step in enabling 3D radiation dosimeters to enter wider use in clinics. Polymer gels and Fricke gels, as well as dosimeters not based around gels, have been characterized for 3D dosimetry over the last two decades. A separate problem is the verification of the best readout method. A number of different imaging modalities (magnetic resonance imaging (MRI), optical CT, x-ray CT and ultrasound) have been suggested for the readout of information from 3D dosimeters. To date only MRI and laser-based optical CT have been characterized in detail. This paper describes some initial steps we have taken in establishing charge coupled device (CCD)-based optical CT as a viable alternative to MRI for readout of 3D radiation dosimeters. The main advantage of CCD-based optical CT over traditional laser-based optical CT is a speed increase of at least an order of magnitude, while the simplicity of its architecture would lend itself to cheaper implementation than both MRI and laser-based optical CT if the camera itself were inexpensive enough. Specifically, we study the following aspects of optical metrology, using high quality test targets: (i) calibration and quality of absorbance measurements and the camera requirements for 3D dosimetry; (ii) the modulation transfer function (MTF) of individual projections; (iii) signal-to-noise ratio (SNR) in the projection and reconstruction domains; (iv) distortion in the projection domain, depth-of-field (DOF) and telecentricity. The principal results for our current apparatus are as follows: (i) SNR of optical absorbance in projections is better than 120:1 for uniform phantoms in absorbance range 0.3 to 1.6 (and better than 200:1 for absorbances 1.0 to 3.5 with the test target and a novel absorbance range extension method), (ii) the spatial resolution is shown to be at worst 0.5 mm (and often better than this) with an associated DOF of 8 cm, (iii) the SNR of uniform phantoms in reconstruction domain is above 80:1 (one standard deviation) over an absorbance dynamic range of 0.3 to 1.6, (iv) the apparatus is telecentric and without distortion. Finally, a sample scan and reconstruction of a scan of a PRESAGE dosimeter are shown, demonstrating the capabilities of the apparatus.

Two-point maximum entropy noise discrimination in spectra over a range of baseline offsets and signal-to-noise ratios

The two-point maximum entropy method (TPMEM) is a useful method for signal-to-noise ratio enhancement and deconvolution of spectra, but its efficacy is limited under conditions of high background offsets. This means that spectra with high average background levels, regions with high background in spectra with varying background levels, and regions of high signal-to-noise ratios are smoothed less effectively than spectra or spectral regions without these conditions. We report here on the cause of this TPMEM limitation and on appropriate baseline estimation and removal procedures that effectively minimize the effects on regularization. We also present a comparative analysis of TPMEM and Savitzky-Golay filtering to facilitate selection of the best technique under a given range of conditions.