Spatial Distortion Correction Research Articles

SpatDistCalib: a GUI Python software for spatial-distortion correction of 2D detectors using splines.

CCD-based X-ray detector systems often suffer from spatial distortions. Reproducible distortions can be quantitatively measured with a calibration grid and described as a displacement matrix or as spline functions. The measured distortion can be used afterwards to undistort raw images or to refine the actual position of each pixel, e.g. for azimuthal integration. This article describes a method using a regular grid, not necessarily orthogonal, to measure the distortions. The graphical user interface (GUI) Python software that is used to implement this method is available under a GPLv3 license on ESRF GitLab, and produces a spline file that is usable with data-reduction software such as FIT2D or pyFAI.

Greenhouse gases monitoring instrument on a GF-5 satellite-II: correction of spatial and frequency-dependent phase distortion.

Interference data obtained by a spatial heterodyne spectrometer (SHS) is subject to various error factors and suffers from complex phase distortion. Traditional phase correction methods, such as the Amplitude, Merzt, and Forman methods, extract phase distortion in the spectral domain and correct it, which cannot effectively correct spatial phase distortion. Through theoretical derivation and numerical simulation, the spatial phase distortion is firstly determined and corrected in the interference domain. The frequency-dependent phase distortion is then extracted in the spectral domain and corrected. This novel phase distortion correction method named the phase decomposition method was applied to the in-orbit interference data of Greenhouse gases Monitoring Instrument-II (GMI-II). Compared with traditional phase correction methods, the root-mean-square error of the spectrum corrected using the phase decomposition method is reduced by 81.37%.

Effect of spatial distortions in head-mounted displays on visually induced motion sickness.

Incomplete optical distortion correction in VR HMDs leads to spatial dynamic distortion, which is a potential cause of VIMS. A perception experiment is designed for the investigation with three spatial distortion levels, with the subjective SSQ, five-scale VIMS level rating, and objective postural instability adopted as the evaluation metrics. The results show that the factor of spatial distortion level has a significant effect on all metrics increments (p<0.05). As the spatial distortion level drops off, the increments of VIMS symptoms decrease. The study highlights the importance of perfect spatial distortion correction in VR HMDs for eliminating the potential VIMS aggravation effect.

Parallel array signal processing technology for spatial phase distortion correction in heterodyne detection.

The spatial phase distortion caused by a rough target causes a decoherence effect which, in turn, produces system sensitivity degradation. The decoherence phenomenon is the primary problem that restricts the application of active optical heterodyne detection, e.g., synthetic aperture radar and long-range coherent laser detection and ranging. By establishing a one-to-one correspondence between the combination of array signals and the system signal-to-noise ratio (SNR), a scheme for spatial phase distortion correction based on the intelligent optimization algorithm is proposed in this paper. The calculation of phase adjustments for each array signal is transformed into an optimization problem for the combination of array signals, experiments are conducted using rough target heterodyne images, and the parallel genetic algorithm (PGA) is used to calculate the phase adjustment of each array element. The results show that the spatial random phase distortion is corrected effectively without prior knowledge, and the PGA achieves an excellent computational performance which, along the efficiency of the proposed technology, has wide-scale implications for the application of active heterodyne detection and optical coherent communication.

Joint Motion Compensation and Distortion Correction for Maneuvering Target Bistatic ISAR Imaging Based on Parametric Minimum Entropy Optimization

Bistatic inverse synthetic aperture radar (Bi-ISAR) can obtain complementary information of moving targets and overcome the inherent imaging limitations of monostatic ISAR. However, the complex motion of maneuvering targets invalidates the assumption that the imaging projection plane (IPP) is constant in conventional Bi-ISAR imaging. The 2-D spatial variant phase errors would be induced. Moreover, the phase errors have a high-order form due to the time-varying bistatic angle and the high maneuvering characteristics of the target. Meanwhile, the linear geometric distortion induced by the bistatic configuration seriously challenges target identification and classification. In this paper, we propose a novel method to compensate for the 2-D spatial variant phase errors and correct the geometric distortion simultaneously for Bi-ISAR imaging based on parametric minimum entropy optimization. First, the signal mode for maneuvering target in the bistatic configuration is developed. Second, based on the developed signal model, we analyze the coupling relationship between the 2-D high-order spatial variant phase errors and the bistatic angle, and establish a parametric minimum entropy optimization model for high-order spatial variant phase errors compensation. Then, an efficient Broyden–Fletcher–Goldfarb–Shanno (BFGS) method is adopted to obtain the optimal solution of spatial variant coefficients. Finally, with the estimated optimal parameters, the integrated processing of 2-D spatial variant phase errors compensation and distortion correction can be realized. This method can simultaneously obtain well-focused and restored Bi-ISAR images of maneuvering targets without selecting prominent scatterers. Experiments based on scattering point simulation data and electromagnetic data verify the effectiveness of the proposed method.

Identification and correction of temporal and spatial distortions in scanning transmission electron microscopy

Scanning transmission electron microscopy (STEM) has become the technique of choice for quantitative characterization of atomic structure of materials, where the minute displacements of atomic columns from high-symmetry positions can be used to map strain, polarization, octahedra tilts, and other physical and chemical order parameter fields. The latter can be used as inputs into mesoscopic and atomistic models, providing insight into the correlative relationships and generative physics of materials on the atomic level. However, these quantitative applications of STEM necessitate understanding the microscope induced image distortions and developing the pathways to compensate them both as part of a rapid calibration procedure for in situ imaging, and the post-experimental data analysis stage. Here, we explore the spatiotemporal structure of the microscopic distortions in STEM using multivariate analysis of the atomic trajectories in the image stacks. Based on the behavior of principal component analysis (PCA), we develop the Gaussian process (GP)-based regression method for quantification of the distortion function. The limitations of such an approach and possible strategies for implementation as a part of in-line data acquisition in STEM are discussed. The analysis workflow is summarized in a Jupyter notebook that can be used to retrace the analysis and analyze the reader's data.

Improved correction by freeform surfaces in prism spectrometer concepts.

The correction of spatial resolution and distortion in imaging spectrometer systems is of great importance due to their significant impact on efficiency and quality. In this study, we analyze the corrective power of freeforms added at different positions in various spectrometer systems for high-performance requirements. The results show that the combination of a freeform prism and a second freeform close to the image has the best correction of distortion while preserving spot size.

Spatial weight matrix in dimensionality reduction reconstruction for micro-electromechanical system-based photoacoustic microscopy

A micro-electromechanical system (MEMS) scanning mirror accelerates the raster scanning of optical-resolution photoacoustic microscopy (OR-PAM). However, the nonlinear tilt angular-voltage characteristic of a MEMS mirror introduces distortion into the maximum back-projection image. Moreover, the size of the airy disk, ultrasonic sensor properties, and thermal effects decrease the resolution. Thus, in this study, we proposed a spatial weight matrix (SWM) with a dimensionality reduction for image reconstruction. The three-layer SWM contains the invariable information of the system, which includes a spatial dependent distortion correction and 3D deconvolution. We employed an ordinal-valued Markov random field and the Harris Stephen algorithm, as well as a modified delay-and-sum method during a time reversal. The results from the experiments and a quantitative analysis demonstrate that images can be effectively reconstructed using an SWM; this is also true for severely distorted images. The index of the mutual information between the reference images and registered images was 70.33 times higher than the initial index, on average. Moreover, the peak signal-to-noise ratio was increased by 17.08% after 3D deconvolution. This accomplishment offers a practical approach to image reconstruction and a promising method to achieve a real-time distortion correction for MEMS-based OR-PAM.

A Small Field, High Resolution γ-Camera System dedicated to SPECT Imaging

A small field, high resolution γ-Camera system dedicated to radiopharmaceutical research and other clinical SPECT (Single Photon Emission Computed Tomography) applications is currently being developed in our group. The system is equipped with the 3” HAMAMATSU R2486 Position Sensitive PhotoMultiplier Tube (PSPMT) with a 16X+16Y-crossed wire anode and various pixelated and ho- mogeneous scintillation crystals. Planar images are created from the recorded charge signals by applying the resistive chain technique. The main part of this work focuses on the development of new correction methods for the improvement of the spatial resolution and the uniformity of the γ-Camera. The spatial distortion correction technique is based on lookup tables with the coordinates of reference points which are selected during the calibration phase of the system for a given set of collimator and scintillation crystal. The applied algorithm incorporates 2D-interpolation tech- niques and has been developed on a full automated graphics environment making use of the HIGZ (High Level Interface to Graphics and ZEBRA) program libraries from CERN. Both correction methods for the spatial distortion and non-uniformity have been applied to phantom images using several combinations of small capillaries filled with water solution of 99mTc. Comparative studies are shown on planar im- ages for different phantom geometries. The method is also extended to tomographic images and the obtained SPECT improvement in resolution is discussed.

Distortion Correction Protocol for Digital Image Correlation after Scanning Electron Microscopy: Emphasis on Long Duration and Ex-Situ Experiments

Recently, scanning electron microscopy (SEM) has been used for digital image correlation (DIC), as micrographs can be acquired with high magnification, providing improved resolution to quantify strain heterogeneities. However, it has been shown by researchers that SEM images can be problematic due to inherent electromagnetic distortions that are not present in optical images. Drift, spatial distortions, and magnification uncertainties are the main issues that can seriously affect the accuracy of localized strain measurements. The present work focuses on long duration experiments, for which images are taken days or weeks apart. We have proposed a systematic procedure to reduce drift, correct spatial distortion, and account for magnification variations between pairs of acquired images. Additionally, SEM parameters are discussed and chosen to increase the signal-to-noise ratio and improve the accuracy of the DIC measurements. The spatial distortion correction increases the repeatability of the correlated values and the precision of the measurements. The implementation for this type of correction is done by applying the measured distortion gradient of a certified grid onto the DIC strain field. The magnification adjustment increases the reliability of the strain maps, ensuring the measurements are in agreement with the actual strain induced during the experiment. We have presented a systematic protocol for ex-situ DIC experiments within the SEM and some basic cross-check procedures that can be performed to evaluate the reliability of the reference grid and the precision of the final strain map.

Automated Model-Based Calibration of Short-Wavelength Infrared (SWIR) Imaging Spectrographs

Among the variety of available hyperspectral imaging systems, the line-scan technique stands out for its short acquisition time and good signal-to-noise ratio. However, due to imperfections in the camera lens and, in particular, optical components of the imaging spectrograph, the acquired images are spatially and spectrally distorted, which can significantly degrade the accuracy of the subsequent hyperspectral image analysis. In this work, we propose and evaluate an automated method for correction of spatial and spectral distortions introduced by a line-scan hyperspectral imaging system operating in the short wavelength infrared (SWIR) spectral range from 1000 nm to 2500 nm. The proposed method is based on non-rigid registration of the distorted and reference images corresponding to two passive calibration objects. The results of the validation show that the proposed method is accurate, efficient, and applicable for calibration of line-scan hyperspectral imaging systems. Moreover, the design of the method and of the calibration objects allows integration with systems operating in diffuse reflectance or transmittance modes.

Focusing and compression of ultrashort pulses through scattering media

Light scattering in inhomogeneous media induces wavefront distortions which pose an inherent limitation in many optical applications. Examples range from microscopy and nanosurgery to astronomy. In recent years, ongoing efforts have made the correction of spatial distortions possible by wavefront shaping techniques. However, when ultrashort pulses are employed scattering induces temporal distortions which hinder their use in nonlinear processes such as in multiphoton microscopy and quantum control experiments. Here we show that correction of both spatial and temporal distortions can be attained by manipulating only the spatial degrees of freedom of the incident wavefront. Moreover, by optimizing a nonlinear signal the refocused pulse can be shorter than the input pulse. We demonstrate focusing of 100fs pulses through a 1mm thick brain tissue, and 1000-fold enhancement of a localized two-photon fluorescence signal. Our results open up new possibilities for optical manipulation and nonlinear imaging in scattering media.

Spatial Distortion Correction and Crystal Identification for MRI-Compatible Position-Sensitive Avalanche Photodiode-Based PET Scanners

Position-sensitive avalanche photodiodes (PSAPDs) are gaining widespread acceptance in modern PET scanner designs, and owing to their relative insensitivity to magnetic fields, especially in those that are MRI-compatible. Flood histograms in PET scanners are used to determine the crystal of annihilation photon interaction and hence, for detector characterization and routine quality control. For PET detectors that use PSAPDs, flood histograms show a characteristic pincushion distortion when Anger logic is used for event positioning. A small rotation in the flood histogram is also observed when the detectors are placed in a magnetic field. We first present a general purpose automatic method for spatial distortion correction for flood histograms of PSAPD-based PET detectors when placed both inside and outside a MRI scanner. Analytical formulae derived for this scheme are based on a hybrid approach that combines desirable properties from two existing event positioning schemes. The rotation of the flood histogram due to the magnetic field is determined iteratively and is accounted for in the scheme. We then provide implementation details of a method for crystal identification we have previously proposed and evaluate it for cases when the PET detectors are both outside and in a magnetic field. In this scheme, Fourier analysis is used to generate a lower-order spatial approximation of the distortion-corrected PSAPD flood histogram, which we call the 'template'. The template is then registered to the flood histogram using a diffeomorphic iterative intensity-based warping scheme. The calculated deformation field is then applied to the segmentation of the template to obtain a segmentation of the flood histogram. A manual correction tool is also developed for exceptional cases. We present a quantitative assessment of the proposed distortion correction scheme and crystal identification method against conventional methods. Our results indicate that our proposed methods lead to a large reduction in manual labor and indeed can routinely be used for calibration and characterization studies in MRI-compatible PET scanners based on PSAPDs.

Methods for increasing the reliability of coordinate determination by the location and imaging systems of endocardial electrodes

Catheter ablation of cardiac arrhythmia sources is subject to a number of technological restrictions due to the absence of direct visual control over the manipulated tool, as well as the impossibility of anatomical imaging of arrhythmogenic zones and estimation of the degree and volume of lesion. Location and imaging systems are used to increase the technological efficiency of catheter ablation. These systems make it possible to visualize the electrode movements in the reconstructed volume without roentgenoscopic monitoring. In this work, methods for correction of spatial distortions occurring during location are suggested and discussed. Methods for compensation of the effect of mechanical movements caused by heart contractions and breathing on the accuracy of determination of coordinates of endocardial electrodes are considered. Methods for stabilizing the coordinate determination system during radio-frequency ablation are suggested.

Study on the clinical application of pulsed DC magnetic technology for tracking of intraoperative head motion during frameless stereotaxy

BackgroundTracking of post-registration head motion is one of the major problems in frameless stereotaxy. Various attempts in detecting and compensating for this phenomenon rely on a fixed reference device rigidly attached to the patient's head. However, most of such reference tools are either based on an invasive fixation technique or have physical limitations which allow mobility of the head only in a restricted range of motion after completion of the registration procedure.MethodsA new sensor-based reference tool, the so-called Dynamic Reference Frame (DRF) which is designed to allow an unrestricted, 360° range of motion for the intraoperative use in pulsed DC magnetic navigation was tested in 40 patients. Different methods of non-invasive attachment dependent on the clinical need and type of procedure, as well as the resulting accuracies in the clinical application have been analyzed.ResultsApart from conventional, completely rigid immobilization of the head (type A), four additional modes of head fixation and attachment of the DRF were distinguished on clinical grounds: type B1 = pin fixation plus oral DRF attachment; type B2 = pin fixation plus retroauricular DRF attachment; type C1 = free head positioning with oral DRF; and type C2 = free head positioning with retroauricular DRF. Mean fiducial registration errors (FRE) were as follows: type A interventions = 1.51 mm, B1 = 1.56 mm, B2 = 1.54 mm, C1 = 1.73 mm, and C2 = 1.75 mm. The mean position errors determined at the end of the intervention as a measure of application accuracy were: 1.45 mm in type A interventions, 1.26 mm in type B1, 1.44 mm in type B2, 1.86 mm in type C1, and 1.68 mm in type C2.ConclusionRigid head immobilization guarantees most reliable accuracy in various types of frameless stereotaxy. The use of an additional DRF, however, increases the application scope of frameless stereotaxy to include e.g. procedures in which rigid pin fixation of the cranium is not required or desired. Thus, continuous tracking of head motion allows highly flexible variation of the surgical strategy including intraoperative repositioning of the patient without impairment of navigational accuracy as it ensures automatic correction of spatial distortion. With a dental cast for oral attachment and the alternative option of non-invasive retroauricular attachment, flexibility in the clinical use of the DRF is ensured.

MO-D-I-609-01: Improved Target Localization in Low Field MR Using Local Weighted Mean(LWM) for Spatial Distortion Correction

Purpose: A methodology using local approximation method is presented for improving spatial distortion correction of Philips Panorama 0.23T MR‐Simulator. The effect on accurate MR based segmentation is evaluated. Method and Materials: Standard T2 MR data was collected using the 0.23T MR‐Simulator. For spatial distortion evaluation/ correction, a standard phantom with dimension of 14″*17″*1″ containing a grid of MR markers at 2.5cm spacing was imaged. The spatial fidelity of the MR data was compared with the physical measurements of marker position using both the vendor supplied spatial distortion correction algorithm and our LWM algorithm, which employs local polynomial fitting and marker centroids serving as control points. The markers are automatically detected using a Gaussian kernel. CT‐MR image registrations using normalized mutual information were applied to estimate the effect of spatial distortion on image registration.Results: Using LWM, the diameter of the imaging region with minimal spatial distortion (marker localization error < 1mm) increased to 300mm, in contrast to the Philips' correction method characterized by diameter=70mm. Visual inspection of clinical imaging data, including a case of craniopharyngioma, indicated such distortion is not readily discernible to the human eye. CT‐MR registration results indicated that the normalized mutual information (NMI) increased about 5% after applying LWM to the MR data compared to using the vendor supplied algorithm. Shifts of up to 3mm were observed in segmentation involving off‐axis target regions between LWM and vendor corrected MR data. Conclusion: LWM provides a significantly superior correction for spatial distortion associated with low field MR imaging compared to the vendor supplied correction. This improves target localization accuracy based on segmentation of off‐axis structures, and increases NMI value of CT‐MR registration. MR imaging with minimal spatial distortion allows the MR‐simulator to be used to monitor tumor regression during radiotherapy.

Correction of spatial distortion in EPI due to inhomogeneous static magnetic fields using the reversed gradient method.

To derive and implement a method for correcting spatial distortion caused by in vivo inhomogeneous static magnetic fields in echo-planar imaging (EPI). The reversed gradient method, which was initially devised to correct distortion in images generated by spin-warp MRI, was adapted to correct distortion in EP images. This method provides point-by-point correction of distortion throughout the image. EP images, acquired with a 3 T MRI system, of a phantom and a volunteer's head were used to test the correction method. Good correction was observed in all cases. Spatial distortion in the uncorrected images ranged up to 4 pixels (12 mm) and was corrected successfully. The correction was improved by the application of a nonlinear interpolation scheme. The correction requires that two EP images be acquired at each slice position. This increases the acquisition time, but an improved signal-to-noise ratio (SNR) is seen in the corrected image. The local SNR gain decreases with increasing distortion. In many EPI acquisition schemes, multiple images are averaged at each slice position to increase the SNR; in such cases the reversed gradient correction method can be applied with no increase in acquisition duration.

Computer-aided radiation therapy simulation: image intensifier spatial distortion correction for large field of view digital fluoroscopy

An accurate method of correcting spatial distortion in digital fluoroscopy images has been developed for generating fluoroscopy-based large field of view images for computer-aided radiation therapy simulation. This method is applicable to arbitrary gantry rotations and arbitrary shifts of the image intensifier relative to the central axis of the x-ray beam. It is therefore suitable for conventional radiation therapy simulation techniques that involve the arbitrary positioning of the image intensifier by the operator. Spatial distortion is modelled as two image intensifier orientation-dependent components, the first resulting from the projection of the x-ray image onto the curved surface of the image intensifier front end, and the second produced by the image intensifier electron optics, interactions with external magnetic fields and the video system. A geometrical model approximates the first component. The second component is modelled by a third-order polynomial transformation. A weighted mean approach is employed to achieve accurate distortion correction when the image intensifier is oriented differently from the calibration orientations. Mean and maximum residual errors (measured in the plane of the isocentre) of 0.4 mm and 1.0 mm respectively have been achieved with just 48 calibration orientations in four dimensions (gantry rotation and lateral, longitudinal and vertical shifts of the image intensifier).

Aberration control in quantitative imaging of botanical specimens by multidimensional fluorescence microscopy

Three dimensional (3‐D) fluorescence microscopes, including conventional instruments with digital deblurring, confocal systems and two‐photon excitation, all exhibit monochromatic and chromatic aberrations. A simple Gaussian model of the aberrated point spread function and optical field for each instrument illustrates spatial distortions and blurring and some unique attenuation effects in confocal and two‐photon microscopy. These properties depend on the manner in which illumination and detection combine to give the overall microscope performance and highlight the importance of both optics and sample aberrations; the specimen must be considered as an optical component of the integrated imaging system.Axial focus distortion, from refractive index boundaries at the sample, can be accurately modelled by a geometric ray tracing programme, considering weighted components across the entire objective lens working NA. The modal z‐focus error, rather than the average of all weighted rays, agrees closely with empirical measurements of axial focus position from test samples. This agreement is particularly close for confocal measurements when NA4 weighting is used in the model calculations, but the situation is more complex for samples with non‐planar refractive boundaries.Calibration of axial attenuation in a botanical sample, arising from the combination of optical sectioning with specimen‐induced spatial distortions and blurring, is possible using an in situ fluorescence sea within a permeabilized preparation. Parametric descriptions of attenuation can be obtained through the guard cell complex of Commelina communis leaf epidermis. Improved images of the 3‐D morphology of stomatal guard cells are then obtained by digital correction of attenuation and spatial distortion. Calibrations can be routinely used to correct experimental data by integration with a structured image file format.

Calibration and correction of spatial distortions in 2D detector systems

Many photon and other radiation 2D detection systems introduce spatial distortions into recorded data. As long as these distortions are to some degree repeatable it is possible to use a grid of holes of known positions to illuminate the detector and calibrate the distortion. Knowledge of this distortion can be used to correct subsequent images. Aspects of calibration grid design are discussed with the aim of achieving optimum results. Cross-correlation with known hole functions is proposed as a method for estimating grid peak centres giving optimum accuracy and efficiency. Strategies to search efficiently complete grids are also presented. Where a physical model of the distortion process is lacking or inadequate, bi-cubic splines are proposed as suitable interpolating functions for defining approximate spatial distortion functions. Bi-cubic splines allow both adequate flexibility to describe arbitrary distortions and, most importantly, to allow efficient calculation for the correction of data. Calibration and correction algorithms have been developed and applied to 2D detector systems. Sample results are presented.