Large Aberrations Research Articles

Differential Lucy-Richardson-Rosen algorithm for near diffraction-limited image restoration assisting by a wavefront sensor

Lucy-Richardson-Rosen algorithm (LR2A) is one of the most important tools for image restoration, especially in computer vision, target imaging and so on. However, the performance of the LR2A can be affected by large optical aberration and imaging noise and even failure under severe environment. To address the mentioned problem, we proposed a new Differential Lucy-Richardson-Rosen Algorithm(D-LR2A) to reduce the influence of optical aberrations and detection noise with advantages of faster speed of convergence and better restoration quality. In the modified optical configuration, a Hartmann-Shack wavefront sensor is employed to measure optical aberration and estimate accurately the Point Spread Function (PSF) of the optical imaging system. The numeric and experimental results show that the proposed method can be used to restore images with large optical aberration and worse noise level. Besides that, it also has faster speed, better restoration quality, and thus easier application as compared to those of LR2A

Large-Dynamic-Range Ocular Aberration Measurement Based on Deep Learning with a Shack-Hartmann Wavefront Sensor.

The Shack-Hartmann wavefront sensor (SHWFS) is widely utilized for ocular aberration measurement. However, large ocular aberrations caused by individual differences can easily make the spot move out of the range of the corresponding sub-aperture in SHWFS, rendering the traditional centroiding method ineffective. This study applied a novel convolutional neural network (CNN) model to wavefront sensing for large dynamic ocular aberration measurement. The simulation results demonstrate that, compared to the modal method, the dynamic range of our method for main low-order aberrations in ocular system is increased by 1.86 to 43.88 times in variety. Meanwhile, the proposed method also has the best measurement accuracy, and the statistical root mean square (RMS) of the residual wavefronts is 0.0082 ± 0.0185 λ (mean ± standard deviation). The proposed method generally has a higher accuracy while having a similar or even better dynamic range as compared to traditional large-dynamic schemes. On the other hand, compared with recently developed deep learning methods, the proposed method has a much larger dynamic range and better measurement accuracy.

Adaptive Optics Methods to Rat Eye Properties: Impact of Pupil Diameter on Wavefront Detection

Achieving a high-quality wavefront sensing light spot and accurate wavefront estimation of the rat eye is still challenging due to its large ocular aberrations and the back reflections from fundus multilayer. Simulation and experiments of rat eye wavefront sensing are conducted to improve the quality of sensing spot for accurate wavefront estimation. The simulation results show that a smaller pupil diameter leads to a high quality of wavefront sensing light spot, and the model rat eye reaches diffractive limitation when the pupil diameter is 0.8 mm. However, the experimental results indicate a different conclusion. Consistent with the simulation results, the quality of the sensing light spot significantly improves when the pupil diameter decreases from 3.6 mm to 1.8 mm. The full width at half maximum (FWHM) of the sensing light spots decreases from 77.36 ± 8.95 μm to 26.78 ± 3.25 μm, and the calculated Strehl ratio increases from 0.007 to 0.396. As the pupil diameter continues to decrease to 1.2 mm, the sensing spot and calculated Strehl ratio continue to improve, while the detected low-order aberrations exhibit a significant increase in both value and variance. This observation suggests that using a half-filled pupil for rat wavefront detection may be a more favorable choice, which assists in obtaining high-resolution retinal images in the rat eye using adaptive optics technology.

Making the unmodulated Pyramid wavefront sensor smart

Almost all current and future high-contrast imaging instruments will use a Pyramid wavefront sensor (PWFS) as a primary or secondary wavefront sensor. The main issue with the PWFS is its nonlinear response to large phase aberrations, especially under strong atmospheric turbulence. Most instruments try to increase its linearity range by using dynamic modulation, but this leads to decreased sensitivity, most prominently for low-order modes, and makes it blind to petal-piston modes. In the push toward high-contrast imaging of fainter stars and deeper contrasts, there is a strong interest in using the PWFS in its unmodulated form. Here, we present closed-loop lab results of a nonlinear reconstructor for the unmodulated PWFS of the Magellan Adaptive Optics extreme (MagAO-X) system based on convolutional neural networks (CNNs). We show that our nonlinear reconstructor has a dynamic range of >600 nm root-mean-square (RMS), significantly outperforming the linear reconstructor that only has a 50 nm RMS dynamic range. The reconstructor behaves well in closed loop and can obtain >80% Strehl at 875 nm under a large variety of conditions and reaches higher Strehl ratios than the linear reconstructor under all simulated conditions. The CNN reconstructor also achieves the theoretical sensitivity limit of a PWFS, showing that it does not lose its sensitivity in exchange for dynamic range. The current CNN’s computational time is 690 µs, which enables loop speeds of >1 kHz. On-sky tests are foreseen soon and will be important for pushing future high-contrast imaging instruments toward their limits.

DeepFocus: fast focus and astigmatism correction for electron microscopy

High-throughput 2D and 3D scanning electron microscopy, which relies on automation and dependable control algorithms, requires high image quality with minimal human intervention. Classical focus and astigmatism correction algorithms attempt to explicitly model image formation and subsequently aberration correction. Such models often require parameter adjustments by experts when deployed to new microscopes, challenging samples, or imaging conditions to prevent unstable convergence, making them hard to use in practice or unreliable. Here, we introduce DeepFocus, a purely data-driven method for aberration correction in scanning electron microscopy. DeepFocus works under very low signal-to-noise ratio conditions, reduces processing times by more than an order of magnitude compared to the state-of-the-art method, rapidly converges within a large aberration range, and is easily recalibrated to different microscopes or challenging samples.

An Efficient Method for Wavefront Aberration Correction Based on the RUN Optimizer

The correction of wavefront aberrations in wavefront sensorless (WFS-less) adaptive optical (AO) systems requires control algorithms that can ensure rapid convergence while maintaining effective correction capabilities. This paper proposes a novel control algorithm based on the RUNge Kutta optimizer (RUN) for WFS-less AO systems that enables the quick and efficient correction of small aberrations, as well as larger aberrations. To evaluate the convergence speed and correction capabilities of a WFS-less AO system based on the RUN control algorithm, we constructed a simulated AO system and an experimental setup with a 97-element deformable mirror (DM), respectively. Additionally, the results obtained with the Particle Swarm Optimization (PSO) algorithm, Differential Evolution Algorithm (DEA), and Genetic Algorithm (GA) are also provided for comparison and analysis. Both the simulated and experimental results consistently demonstrated that our proposed method outperformed several competing algorithms in terms of correction performance and convergence speed. Furthermore, the experimental results further validate the effectiveness of our control algorithm in scenarios involving significant aberrations.

Mutual aid instead of mutual restraint: interactive probing for topological charge and phase of a vortex beam of large aberrations

An imperfect propagation environment or optical system would introduce wavefront aberrations to vortex beams. The phase aberrations and orbital angular momentum in a vortex beam are proved to be mutually restrictive in parameter measurement. Aberrations make traditional topological charge (TC) probing methods ineffective while the phase singularity makes phase retrieval difficult due to the aliasing between the wrapped phase jump and the vortex phase jump. An interactive probing method is proposed to make measurements of the aberrated phase and orbital angular momentum in a vortex beam assist rather than hinder each other. The phase unwrapping is liberated from the phase singularity by an annular shearing interference technique while the TC value is determined by a Moiré technique immune to aberrations. Simulation and experimental results proving the method effective are presented. It is of great significance to judge the characteristics of vortex beams passing through non-ideal environments and optical systems.

A Holographic Broadband Achromatic Metalens

AbstractMetalens with nanostructured optical elements are designed to control wavefront shaping at the wavelength‐scale thickness. However, most metalens still suffer from large chromatic aberrations due to phase dispersion, limiting their wide applications for multiple wavelengths. Here, avoiding complex resonant designs or multiple‐layer nanostructures, a simple broadband achromatic metalens by holographic diffraction in the visible spectrum is demonstrated. The hyperbolic phase distributions of multiple discrete wavelengths within a shared aperture and fabricate a broadband achromatic diffractive metalens by flexible direct‐laser‐writing technique is randomly interleaved. The designed polarization‐insensitive metalens modulate the light field by changing the height of the artificial neuron phase units to achieve average focusing efficiencies of 55% in the visible spectrum. This holographic design concept can pave the way to expand achromatic metalenses to multiple spectra.

10049-GGE-3 CHARACTERISTICS OF CHROMOSOMAL ABERRATIONS IN GLIOMAS AND THEIR IMPACT ON RECURRENCE

Abstract INTRODUCTION Chromosome instability is the inability to evenly distribute sister chromatids during mitosis, which leads to chromosomal numerical/structural abnormalities and increases the genetic heterogeneity of the tumor. In this study, we investigated the association between chromosome aberration characteristics and recurrence in clinical specimens of gliomas using the Spectral Karyotyping. METHODS Chromosome karyotypes were analyzed for a total of 121 cells from 26 gliomas (Glioblastoma 14, PXA 3, Astrocytoma 5, Oligodendroglioma 3, Ependymoma 1, 18 primary cases and 8 recurrent cases) removed at our hospital. In addition, each case was quantitatively analyzed for numerical aberrations/ cell (AS: Aneuploidy score), structural abnormalities/ cell (SS: Structural abnormality score), and karyotype concordance rate between cells /case (HS: Heterogeneity Score) were quantitatively analyzed. RESULTS In the analysis of all cases, numerical aberrations in chromosomes X and 7 (21.5%/16.9%) and structural aberrations in chromosomes 1, 4, and 5 (>10.0%) were highly prevalent, with structural aberrations in large chromosomes and numerical aberrations in small chromosomes. On the other hand, quantitative analysis showed that the mean for the first occurrence (18 cases); AS: 2.22±0.94/ SS: 1.48±0.96/ HS: 22.2±7.41, and for the recurrence (8 cases); AS: 4.68±1.75/ SS: 7.50±1.44/ HS: 55.0±11.1, indicating that numerical and structural abnormalities were more common in the recurrent lesions The recurrent lesions showed more numerical and structural abnormalities and higher intra-tumor heterogeneity. In addition, in cases in which the primary/recurrent lesions were analyzed in pairs, the frequency of numerical and structural chromosomal abnormalities was higher in the recurrent lesions. DISCUSSION This study clarified the characteristics of chromosomal aberrations in each pathological classification of gliomas and suggested the involvement of chromosomal instability in the recurrence process. We look forward to further clarification of the pathogenesis of gliomas with a focus on chromosomal instability.

Analysis of Imaging Characteristics of Wide-field Lobster Eye Lens

The lobster-eye lens is a reflected type focusing optics. It can be used for backscattering imaging that is a single-sided access technology for homeland security, detection of improvised explosive devices, non-destructive testing, and medical imaging. The aim of this study was to investigate the imaging characteristic of meridional lobster-eye lens with a planar imaging surface. The larger the field of view, the greater the spherical aberration, and the larger the field curvature of the edge field of view. Both spherical aberration and field curvature increase the size of the focal spot, and the images become blurry. Rays with a large angle of grazing incidence have large spherical aberration and curvature. The reflectivity of these rays drops sharply as the energy of photons increases. Therefore, spherical aberration and field curvature have a greater effect on photons with low energy. These conclusions can help improve the design of a lobster-eye lens for wide-field imaging applications.

Sb2S3-Based Dynamically Tuned Color Filter Array via Genetic Algorithm.

Color displays have become increasingly attractive, with dielectric optical nanoantennas demonstrating especially promising applications due to the high refractive index of the material, enabling devices to support geometry-dependent Mie resonance in the visible band. Although many structural color designs based on dielectric nanoantennas employ the method of artificial positive adjustment, the design cycle is too lengthy and the approach is non-intelligent. The commonly used phase change material Ge2Sb2Te5 (GST) is characterized by high absorption and a small contrast to the real part of the refractive index in the visible light band, thereby restricting its application in this range. The Sb2S3 phase change material is endowed with a wide band gap of 1.7 to 2 eV, demonstrating two orders of magnitude lower propagation loss compared to GST, when integrated onto a silicon waveguide, and exhibiting a maximum refractive index contrast close to 1 at 614 nm. Thus, Sb2S3 is a more suitable phase change material than GST for tuning visible light. In this paper, genetic algorithms and finite-difference time-domain (FDTD) solutions are combined and introduced as Sb2S3 phase change material to design nanoantennas. Structural color is generated in the reflection mode through the Mie resonance inside the structure, and the properties of Sb2S3 in different phase states are utilized to achieve tunability. Compared to traditional methods, genetic algorithms are superior-optimization algorithms that require low computational effort and a high population performance. Furthermore, Sb2S3 material can be laser-induced to switch the transitions of the crystallized and amorphous states, achieving reversible color. The large chromatic aberration ∆E modulation of 64.8, 28.1, and 44.1 was, respectively, achieved by the Sb2S3 phase transition in this paper. Moreover, based on the sensitivity of the structure to the incident angle, it can also be used in fields such as angle-sensitive detectors.

ONT long-read WGS for variant discovery and orthogonal confirmation of short read WGS derived genetic variants in clinical genetic testing.

Technological advances in Next-Generation Sequencing dramatically increased clinical efficiency of genetic testing, allowing detection of a wide variety of variants, from single nucleotide events to large structural aberrations. Whole Genome Sequencing (WGS) has allowed exploration of areas of the genome that might not have been targeted by other approaches, such as intergenic regions. A single technique detecting all genetic variants at once is intended to expedite the diagnostic process while making it more comprehensive and efficient. Nevertheless, there are still several shortcomings that cannot be effectively addressed by short read sequencing, such as determination of the precise size of short tandem repeat (STR) expansions, phasing of potentially compound recessive variants, resolution of some structural variants and exact determination of their boundaries, etc. Therefore, in some cases variants can only be tentatively detected by short reads sequencing and require orthogonal confirmation, particularly for clinical reporting purposes. Moreover, certain regulatory authorities, for example, New York state CLIA, require orthogonal confirmation of every reportable variant. Such orthogonal confirmations often involve numerous different techniques, not necessarily available in the same laboratory and not always performed in an expedited manner, thus negating the advantages of "one-technique-for-all" approach, and making the process lengthy, prone to logistical and analytical faults, and financially inefficient. Fortunately, those weak spots of short read sequencing can be compensated by long read technology that have comparable or better detection of some types of variants while lacking the mentioned above limitations of short read sequencing. At Variantyx we have developed an integrated clinical genetic testing approach, augmenting short read WGS-based variant detection with Oxford Nanopore Technologies (ONT) long read sequencing, providing simultaneous orthogonal confirmation of all types of variants with the additional benefit of improved identification of exact size and position of the detected aberrations. The validation study of this augmented test has demonstrated that Oxford Nanopore Technologies sequencing can efficiently verify multiple types of reportable variants, thus ensuring highly reliable detection and a quick turnaround time for WGS-based clinical genetic testing.

Quantifying the morphology of eyeballs with posterior staphyloma with Zernike polynomials.

Purpose: To quantify the morphology of eyeballs with posterior staphyloma (PS) with Zernike decomposition and to explore the association between Zernike coefficients with existing PS classification. Methods: Fifty-three eyes with high myopia (HM, ≤-6.00D) and 30 with PS were included. PS was classified with traditional methods based on OCT findings. Eyeballs' morphology was obtained with 3D MRI, from which the height map of the posterior surface was extracted. Zernike decomposition was performed to derive the coefficients of the 1st-27th items, which were compared between HM and PS eyes with the Mann-Whitney-U test. Receiver operating characteristics (ROC) analysis was used to test the effectiveness of using Zernike coefficients to discriminate PS from HM. Results: Compared to HM eyeballs, PS eyeballs had significantly increased vertical and horizontal tilt, oblique astigmatism, defocus, vertical and horizontal coma, and higher order aberrations (HOA) (all Ps < 0.05). HOA was the most effective in PS classification with an area under the ROC curve (AUROC) value of 0.977. Among the 30PS, 19 were the wide macular type with large defocus and negative spherical aberration; 4 were the narrow macular type with positive spherical aberration; 3 were inferior PS with greater vertical tilt, and 4were peripapillary PS with larger horizontal tilt. Conclusion: PS eyes have significantly increased Zernike coefficients, and HOA is the most effective parameter to differentiate PS from HM. The geometrical meaning of the Zernike components showed great accordance with PS classification.

Imagining the Hebrew Ode: On Robert Lowth’s Biblical Species

Abstract: The subject of this article is the reception history of biblical genres, or the metapoetics of genre-making. It argues that the seemingly fixed presentations of the genres of biblical poetry in the twentieth century—as in Robert Alter’s classic guide to biblical Hebrew poetry—emerge from an eighteenth-century encounter: the English exegete Robert Lowth’s dramatic attempt to fit Greek and Roman generic models to the Hebrew text. Lowth’s resulting genres, or what he called the “species” of biblical poetry, were shaped both by the parallels he discovered between classical and Hebrew traditions, and by the small and large aberrations he faced in his process of translation. The article focuses on the characterization of a poetic form that never existed: the ancient Hebrew ode. Although, in this case, Lowth fails in his biblical scholarship, his Hebrew ode demonstrates the spirit of his creative project. By fitting Hebrew poetry to neoclassical models, Lowth subtly transformed neoclassical categories and possibilities, opening up new imaginative expanses within the lyrical mode and preparing the way for a more flexible, complex, and emotionally sophisticated Romantic lyric.

Direct model-based wavefront sensorless method with a fixed number of measurements

In wavefront sensorless (WFSL) adaptive optics, the intensity image in the observation plane, instead of the wavefront sensor, is utilised to estimate the input aberration. The number of intensity measurements is critical for applications with ever-changing phase aberration, such as astronomical imaging. This paper details two direct WFSL methods that need a fixed number of intensity measurements to estimate the input aberration. The proposed methods adopt a zonal approach rather than a modal one to estimate the phase aberration. Simulation results demonstrate that after applying the proposed methods, the aberration correction percentage can rise by approximately 70% for large aberrations.

26. Identification of novel genomic structural variations in Angiosarcoma by Optical Genome Mapping

Angiosarcomas are malignant vascular tumors with a number of known molecular aberrations identified by standard technologies, such as FISH and next generation sequencing. However, potentially clinically significant large genomic aberrations, such as gene fusion, large amplification and deletions, may not be detectable by these technologies. To gain further insights into the genomic landscape of angiosarcoma, we performed optical genome mapping (OGM) of 3 primary human angiosarcoma cell lines. OGM analysis of these cells revealed multiple unique structural aberrations, including large insertions/deletions, inversions, duplications, inter-chromosomal and intra-chromosomal translocations. Further analysis showed a 354-Kb deletion in Plexin D1 gene locus that regulates the migration of endothelial cells and is required for normal development of the heart and vasculature; reciprocal t(4;9) translocation in UGT8 (UDP Glycosyltransferase 8) gene locus that is involved in biosynthesis of galactocerebrosidase; reciprocal t(6;22) translocation involving HIRA (Histone Cell Cycle Regulator) and EYS (Eyes Shut Homolog) gene loci; and 14 Mb inversion interrupting RYR2 (Ryanodine Receptor 2) and TAF1A (TATA-Box Binding Protein Associated Factor) gene loci. These findings demonstrate the utility of optical genome mapping as a new tool to uncover large genomic structural variations to better understand the molecular pathogenesis of malignant vascular tumors. Future studies are aimed to determine the biological significance of these structural variations in angiosarcoma.

The kinetics of blast clearance are associated with copy number alterations in childhood B-cell acute lymphoblastic leukemia

We analyzed the pattern of whole-genome copy number alterations (CNAs) and their association with the kinetics of blast clearance during the induction treatment among 195 pediatric patients with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) who displayed intermediate or high levels of minimal residual disease (MRD). Using unsupervised hierarchical clustering of CNAs > 5 Mbp, we dissected three clusters of leukemic samples with distinct kinetics of blast clearance [A – early slow responders (n=105), B – patients with persistent leukemia (n=24), C – fast responders with the low but detectable disease at the end of induction (n=66)] that corresponded with the patients’ clinical features, the microdeletion profile,the presence of gene fusions and patients survival. Low incidence of large CNAs and chromosomal numerical aberrations occurred in cluster A which included ALL samples showing recurrent microdeletions within the genes encoding transcription factors (i.e., IKZF1, PAX5, ETV6, and ERG), DNA repair genes (XRCC3 and TOX), or harboring chromothriptic pattern of CNAs. Low hyperdiploid karyotype with trisomy 8 or hypodiploidy was predominantly observed in cluster B. Whereas cluster C included almost exclusively high-hyperdiploid ALL samples with concomitant mutations in RAS pathway genes. The pattern of CNAs influences the kinetics of leukemic cell clearance and selected aberrations affecting DNA repair genes may contribute to BCP-ALL chemoresistance.

End-to-End Optimization of an Achromatic Diffractive Optical Element Array for Integral Imaging Three-Dimensional Display

Diffractive optical element (DOE) array promises compact shape for full-parallax integral imaging three-dimensional (3D) display. However, DOEs suffer from large chromatic aberration due to the strong wavelength-dependent nature of diffraction phenomena that degrade the quality of reconstructed 3D images. An end-to-end DOE optimization approach is proposed to reduce chromatic aberration for integral imaging. The end-to-end optimization framework includes RGB pre-processing convolutional neural networks and achromatic optics optimization design of rotationally symmetric DOE. An optical display model based on diffractive optics is proposed to analyze the integral imaging 3D display process for achromatic optical optimization design. The pre-processed elemental image arrays are modulated by an optimized DOE array to reconstruct the achromatic 3D images. A 3D artifacts scene without chromatic aberration is reconstructed in different views with the proposed method, and both peak signal to noise ratio (PSNR) and structural similarity (SSIM) are improved compared to the conventional Fresnel lens DOE.

A Method Used to Improve the Dynamic Range of Shack-Hartmann Wavefront Sensor in Presence of Large Aberration.

With the successful application of the Shack–Hartmann wavefront sensor in measuring aberrations of the human eye, researchers found that, when the aberration is large, the local wavefront distortion is large, and it causes the spot corresponding to the sub-aperture of the microlens to shift out of the corresponding range of the sub-aperture. However, the traditional wavefront reconstruction algorithm searches for the spot within the corresponding range of the sub-aperture of the microlens and reconstructs the wavefront according to the calculated centroid, which leads to wavefront reconstruction errors. To solve the problem of the small dynamic range of the Shack–Hartmann wavefront sensor, this paper proposes a wavefront reconstruction algorithm based on the autocorrelation method and a neural network. The autocorrelation centroid extraction method was used to calculate the centroid in the entire spot map in order to obtain a centroid map and to reconstruct the wavefront by matching the centroid with the microlens array through the neural network. This method breaks the limitation of the sub-aperture of the microlens. The experimental results show that the algorithm improves the dynamic range of the first 15 terms of the Zernike aberration reconstruction to varying degrees, ranging from 62.86% to 183.87%.

Region-correlation algorithm with improved dynamic range and reconstruction accuracy for extended object wavefront sensing.

The correlation Shack-Hartmann wavefront sensor (SHWFS) is widely used in many fields in addition to solar adaptive optics. The requirement for the SHWFS dynamic range increases with the diameter of the telescope, which means a larger detector array is needed. However, the size of the detector would be restricted by the high frame rate needed for the solar observation. To solve this problem, a new, to the best of our knowledge, method called the region-correlation algorithm (RCA) is proposed. In this method, the sub-image array is divided into several regions, and the slopes of sub-apertures are calculated by referring to a selected sub-image in each region. Note that the final slope over a sub-aperture is obtained by combining the relative slopes between the selected sub-image in different regions. The dynamic range in each region is similar to the conventional correlation algorithm, and the final dynamic range of the RCA would be accumulated from those of the regions. The reconstruction accuracy under large aberration would also be improved due to the extended dynamic range. Meanwhile, the RCA does not require any extra device and the increase in calculation time resulting from the RCA is acceptable. The results of numerical simulation and experiment, compared with conventional correlation algorithm, confirm the advantages in the performance of the RCA as well.