Contrast Inversion Research Articles

NIMG-66. DEFINING PROGRESSIVE DISEASE: LOCALIZING VOXEL-AT-RISK ON MAGNETIC RESONANCE IMAGING USING DEEP LEARNING

Abstract Follow-up magnetic resonance imaging (MRI) of post-treatment glioblastoma (GBM) can be diagnostically challenging in differentiating progressive disease (PD) from coexisting treatment-related changes. The study aim was to train a machine learning model using multiple MRI timepoints from treated GBM patients with subsequent PD or at least six months of tumor-like, persistently stable disease (SD) to estimate PD risk. A retrospective, post-treatment GBM cohort (n=189) with 453 timepoints was identified with available MRI sequences (T1-weighted with and without contrast, T2-weighted, and fluid-attenuated inversion recovery). PD cases (n=154) showed new, enhancing PD followed by death within 3-6 months; timepoints included the MRI on the PD diagnosis date and the one directly prior. SD cases (n=35) exhibited stable, tumor-like enhancement over timepoints. Cases underwent voxel-wise annotation of PD versus SD. A multiclass, three-dimensional nnU-Net was trained to label voxels as PD, SD, or neither using timepoint sequences with five-fold cross-validation. Model performance was assessed using the ratio of predicted PD/SD voxels compared to each case’s actual PD or SD status. Classification accuracy of PD versus SD status, PD case-wise sensitivity and specificity, and a Receiver Operating Characteristic (ROC) analysis using the PD/SD ratio were presented. The five-fold model ensemble was evaluated on a holdout test set. Validation set performance showed 74.3% accuracy, 0.73 PD case-wise sensitivity, and 0.80 specificity. The holdout set exhibited 79.8% accuracy, 0.81 sensitivity, and 0.78 specificity for PD cases. The ROC analysis showed an area under the curve of 0.80 and 0.83 on the validation and holdout sets, respectively. The model showed high performance and classification accuracy in predicting which voxels were at risk of PD in post-treatment GBM cases. The model also differentiated between PD and SD regions. The model’s predicted PD/SD ratio may be clinically used to stratify patients’ PD risk.

One-dimensional photonic crystal enhancing spin-to-orbital angular momentum conversion for single-particle tracking

Single-particle tracking (SPT) is an immensely valuable technique for studying a variety of processes in the life sciences and physics. It can help researchers better understand the positions, paths, and interactions of single objects in systems that are highly dynamic or require imaging over an extended time. Here, we propose an all-dielectric one-dimensional photonic crystal (1D PC) that enhances spin-to-orbital angular momentum conversion for three-dimensional (3D) SPTs. This well-designed 1D PC can work as a substrate for optical microscopy. We introduce this effect into the interferometric scattering (iSCAT) technique, resulting in a double-helix point spread function (DH-PSF). DH-PSF provides more uniform Fisher information for 3D position estimation than the PSFs of conventional microscopy, such as encoding the axial position of a single particle in the angular orientation of DH-PSF lobes, thus providing a means for 3D SPT. This approach can address the challenge of iSCAT in 3D SPT because DH-PSF iSCAT will not experience multiple contrast inversions when a single particle travels along the axial direction. DH-PSF iSCAT microscopy was used to record the 3D trajectory of a single microbead attached to the flagellum, facilitating precise analysis of fluctuations in motor dynamics. Its ability to track single nanoparticles, such as 3D diffusion trajectories of 20 nm gold nanoparticles in glycerol solution, was also demonstrated. The DH-PSF iSCAT technique enabled by a 1D PC holds potential promise for future applications in physical, biological, and chemical science.

Quantitative analysis of the contrast modulation for multilateral shearing interferometers

Multilateral shearing interferometers (multi-LSIs) utilize the phase difference information of multiple shear directions with high accuracy and strong noise resistance. However, the interferogram fringe contrast of multi-LSIs can reverse due to the effect of contrast modulation, leading to incorrect measurement result. This issue has lacked comprehensive quantitative research to effectively guide the elimination of its effects. In this work, a quantitative analysis of the contrast modulation is proposed. This paper rigorously derives contrast modulation function, analyzing the effect of aberration and shear ratio on it. It is the first time that a quantitative theoretical model of aberration measurement range and shear ratio has been established, offering guidance in practical application for precise shear ratio adjustment to eliminate modulation effect and extend measurement range. By eliminating modulation effects, phase difference information from multiple directions can be effectively utilized, maximizing the benefits of multi-LSIs. In simulation and experiment, the distribution of fringe contrast reversal bands and the variation of aberration measurement range with shear ratio are consistent with theoretical analysis, which verifies the validity of the proposed approach. This approach aims to address the issue of interferogram fringe contrast inversion caused by modulation in multi-LSIs, providing a theoretical basis and practical guidance for precise measurement.

T1 contrast versus fluid-attenuated inversion recovery contrast technique for evaluation of cerebral tuberculosis

Objectives: T2-weighted (T2W) fluid-attenuated inversion recovery (FLAIR), a traditional magnetic resonance imaging (MRI) technique, is regarded as one of the most effective methods for examining brain disorders. The identification of brain pathologies can be significantly aided by T2 FLAIR and T1 post-contrast imaging. However, lesion enhancement is occasionally inconspicuous on T1-weighted image. Hence, for the evaluation of brain disorders, a MRI approach known as FLAIR contrast would combine the benefits of T2W FLAIR with contrast-enhancement on a single picture. Material and Methods: After obtaining clearance from the Institution’s Ethics Committee, contrast-enhanced MRI (CE-MRI) brain of 20 patients was taken for the study. CE-MRI was performed using 1.5 Tesla Intera PHILIPS with intravenous administration of gadolinium at approximately 0.1 mL/kg/body at a rate of 10 mL/15 s. Results: This study showed a better appreciation of lesion conspicuity when compared to prior T1 contrast images. However, there was no significant difference in the number of lesions, lesion extension, and degree of contrast-enhancement on comparison with T1 contrast images. Conclusion: T1 FLAIR contrast shows a better appreciation of lesion conspicuity when compared to T1 contrast images. Post-contrast FLAIR imaging is a valuable adjunct to post-contrast T1W imaging and effectively delineates cerebral tubercular pathologies. However, T1 FLAIR cannot be used as a replacement for conventional T1 fat saturated post-contrast imaging.

Is Dissection and Preservation of Adherent Popliteal Vessels From a Posterior Soft Tissue Mass Associated With a Higher Proportion of Local Recurrence in Patients With a Distal Femoral Osteosarcoma?

Is Dissection and Preservation of Adherent Popliteal Vessels From a Posterior Soft Tissue Mass Associated With a Higher Proportion of Local Recurrence in Patients With a Distal Femoral Osteosarcoma?

Contrast inversion of ferrite and pearlite in a sweet corrosion environment

In-situ optical imaging in a confocal Raman system of a pipeline steel under sweet corrosion environmental conditions typical of a commercial environment (NaCl brine, pH 6.8, temp, 80 °C, low oxygen, open circuit potential) revealed contrast inversion of ferrite and pearlite microdomains as compared to their 3% Nital etched counterpart. This behaviour is in excellent agreement with the time resolved mineralogy growth profile obtained from in-situ confocal Raman and also complemented by AFM and SEM analysis of the surface roughness and corresponding morphology. The data presented here provides new insight into the process of sweet corrosion scaling in a ferritic-pearlitic microstructure steel.

3D reconstruction of unstained weakly scattering cells from a single defocused hologram.

We investigate the problem of 3D complex field reconstruction corresponding to unstained red blood cells (RBCs) with a single defocused off-axis digital hologram. The main challenge in this problem is the localization of cells to the correct axial range. While investigating the volume recovery problem for a continuous phase object like the RBC, we observe an interesting feature of the backpropagated field that it does not show a clear focusing effect. Therefore, sparsity enforcement within the iterative optimization framework using a single hologram data frame cannot effectively restrict the reconstruction to the true object volume. For phase objects, it is known that the amplitude contrast of the backpropagated object field at the focus plane is minimum. We use this information available in the recovered object field in the hologram plane to device depth-dependent weights that are proportional to the inverse of amplitude contrast. This weight function is employed in the iterative steps of the optimization algorithm to assist the object volume localization. The overall reconstruction process is performed using the mean gradient descent (MGD) framework. Experimental illustrations of 3D volume reconstruction of the healthy as well as malaria-infected RBCs are presented. A test sample of polystyrene microsphere bead is also used to validate the axial localization capability of the proposed iterative technique. The proposed methodology is simple to implement experimentally and provides an approximate tomographic solution, which is axially restricted and consistent with the object field data.

Fine structure of the charge density wave in bulk VTe2

Vanadium ditelluride (VTe2) has been intensively explored to understand the charge density wave (CDW) phase and its connection to magnetic properties. Here, we conduct a systematic study to understand the fine structure of CDW via scanning tunneling microscopy (STM) combined with density functional theory (DFT) calculations. STM topograph at 79 K shows that a CDW phase in VTe2 has a stripe modulation with 3 × 1 periodicity, following the double zigzag chain of distorted Te lattices. Interestingly, the 3 × 1 CDW modulation undergoes contrast inversion between filled and empty state topographs. Atomistic features and contrast changes of CDW observed in STM are clearly reproduced in our DFT simulation images. Charge distribution calculation indicates that the spatial extension and density of Te 5p orbitals have strong variations with filled and empty states, explaining the fine structure of 3 × 1 CDW in VTe2. Our finding provides an inspiring insight to further research on the less explored electronic structure of VTe2.

(Digital Presentation) The Role of Steel Microstructures on Sweet Corrosion Scaling By in Situ Confocal Raman

Confocal Raman imaging and spectroscopy has been used in a custom-made flow-cell to map in-situ spatial and temporal growth of siderite and chukanovite on pipeline steel in a hot brine environment, under conditions typical of commercial interest (pH 6.8, temp 80oC, oxygen conc < 10 ppb, 0.5 M NaCl, open circuit potential (OCP)). Ferrite and pearlite domains are found to exhibit an interesting contrast (colour) inversion under sweet environmental conditions compared to their Nital etched contrast – confirmed by identifying the shapes and surrounding of the domains before and after exposure to two different conditions. Ferrite and pearlite phases are found to exhibit differing evolution of the corrosion scale mineralogy, and phase transformation. The process starts by revealing the microstructural phase constituents, significantly the interphase boundaries are identified as the primary sites for scale formation. The ferritic phase forms pure siderite scale while the pearlitic phase shows both siderite and chukanovite scales, with chukanovite transforming into siderite over time. LPR profiles reveal that for carbon steel with a higher pearlite fraction the initial corrosion rate is higher, followed by a faster drop when compared to steel with lower pearlite fraction! Figure 1

The Mechanistic Determination of Doping Contrast from Fermi Level Pinned Surfaces in the Scanning Electron Microscope Using Energy-Filtered Imaging and Calculated Potential Distributions

Abstract Secondary electron (SE) doping contrast in the scanning electron microscope is correlated with Fermi level pinned surfaces of Si samples prepared using HF-based wet-chemical treatment or focused ion beam (FIB) micromachining en route to quantitative dopant profiling. Using energy-resolved SE imaging techniques and finite-element analyses of surface states and surface junction potentials, we clarified the surface band-bending effects post-NH4F-treatment, consistent with brighter p-contrast from degenerately doped (&amp;gt;1019 cm−3) regions. In general, SE spectromicroscopy scan measurements unambiguously indicated heavy suppression of patch fields, while the empirical discovery of scan frequency-modulated contrast inversion due to Chee et al. [Springer Proceedings in Physics, 120, pp. 407–410 (2008)] is ascribable to competing fixed oxide charge and dynamic charge injection phenomena (particularly at dwell times &amp;gt;29 μs). Leveraging numerical simulations of electric potentials and variable-voltage experimental data, the theoretical model based on amorphization damage-mediated Fermi level pinning is elucidated for Ga+ FIB-processed site-specific doping contrast on patch field-free surfaces. This work successfully argues against the notion that doping contrast ultimately or exclusively entails patch fields or adventitious metal–semiconductor contacts.

Nondestructive Evaluation of Composite Bonding Structure Used in Electrical Insulation Based on Active Infrared Thermography.

Nondestructive testing and evaluation of composite insulating components of electrical equipment is extremely necessary for assuring the safety of a power system. However, most existing nondestructive testing methods are not applicable for fast and effective live detection due to their time-consuming operation, high cost, and contact or near-field measurement. In this work, the effectiveness of active infrared thermography was investigated for detecting defects in silicone rubber (SIR)–fiber-reinforced plastic (FRP) bonding structures, which have been commonly used in insulating components of power equipment. The effectiveness of differential thermal image for enhancing the contrast of defective and sound areas and eliminating additive noise was demonstrated. Particularly, frame difference thermal image obtained by subtracting two differential thermal images extracting from respectively before and after the contrast inversion was proposed to enhance defect identification. The results revealed that defects of various sizes and depths such as voids, cracks, and interface disbonding of the SIR–FRP bonding structure were accurately detected by thermographic data. With the advantages of a quick and simple process, safety, universal applicability, visual results, far-field measurement, and quantitative defect estimation capabilities, active infrared thermography would be quite promising for live detection of electrical equipment.

Robustness of the unidirectional stripe order in the kagome superconductor CsV3Sb5

V-based kagome materials AV3Sb5 (A = K, Rb, Cs) have attracted much attention due to their novel properties such as unconventional superconductivity, giant anomalous Hall effect, charge density wave (CDW) and pair density wave. Except for the 2a 0 × 2a 0 CDW (charge density wave with in-plane 2 × 2 superlattice modulation) in AV3Sb5, an additional 1 × 4 (4a 0) unidirectional stripe order has been observed at the Sb surface of RbV3Sb5 and CsV3Sb5. However, the stability and electronic nature of the 4a 0 stripe order remain controversial and unclear. Here, by using low-temperature scanning tunneling microscopy/spectroscopy (STM/S), we systematically study the 4a 0 stripe order on the Sb-terminated surface of CsV3Sb5. We find that the 4a 0 stripe order is visible in a large energy range. The STM images with positive and negative bias show contrast inversion, which is the hallmark for the Peierls-type CDW. In addition, below the critical temperature about 60 K, the 4a 0 stripe order keeps unaffected against the topmost Cs atoms, point defects, step edges and magnetic field up to 8 T. Our results provide experimental evidences on the existence of unidirectional CDW in CsV3Sb5.

Imaging biological samples by integrated differential phase contrast (iDPC) STEM technique

Scanning transmission electron microscopy (STEM) is a powerful imaging technique and has been widely used in current material science research. The attempts of applying STEM (annual dark field (ADF)-STEM or annular bright field (ABF)-STEM) into biological research have been going on for decades while applications have still been limited because of the existing bottlenecks in dose efficiency and non-linearity in contrast. Recently, integrated differential phase contrast (iDPC) STEM technique emerged and achieved a linear phase contrast imaging condition, while resolving signals of light elements next to heavy ones even at low electron dose. This enables successful investigation of beam sensitive materials. Here, we investigate iDPC-STEM advantages in biology, in particular, chemically fixed and resin embedded biological tissues. By comparing results to the conventional TEM, we have found that iDPC-STEM not only shows better contrast but also resolves more structural details at molecular level, including conditions of extremely low dose and minimal heavy-atom staining. We also compare iDPC-STEM with ABF-STEM and found that contrast of iDPC-STEM is even further improved, moderately in lower frequency domains while highly with preserving high frequency biological structural details. For thick sample sections, iDPC-STEM is particularly advantageous. It avoids contrast inversion canceling effects, and by adjusting the depth of focus, fully preserves the contrast of structural details along with the sample. In addition, using depth-sectioning, iDPC-STEM enables resolving in-depth structural variation. Our results suggest that iDPC-STEM have the place and advantages within the future biological research.

Real-space observation of incommensurate spin density wave and coexisting charge density wave on Cr (001) surface

In itinerant magnetic systems, a spin density wave (SDW) state can be induced by Fermi surface nesting and electron-electron interaction. It may intertwine with other orders such as charge density wave (CDW), while their relation is still yet to be understood. Here via spin-polarized scanning tunneling microscopy, we directly observed long-range spin modulation on Cr(001) surface, which corresponds to the well-known incommensurate SDW of bulk Cr. It displays 6.0 nm in-plane period and anti-phase behavior between adjacent (001) planes. Meanwhile, we simultaneously observed the coexisting CDW with half the period of SDW. Such SDW/CDW have highly correlated domain structures and are in-phase. Surprisingly, the CDW displays a contrast inversion around a density-of-states dip at −22 meV, indicating an anomalous CDW gap opened below EF. These observations support that the CDW is a secondary order driven by SDW. Our work is not only a real-space characterization of incommensurate SDW, but also provides insights on how SDW and CDW coexist.

Optically Enhanced Electric Field Sensing Using Nitrogen-Vacancy Ensembles

Nitrogen-vacancy (NV) centers in diamond have shown promise as inherently localized electric-field sensors, capable of detecting individual charges with nanometer resolution. Working with NV ensembles, we demonstrate that a detailed understanding of the internal electric field environment enables enhanced sensitivity in the detection of external electric fields. We follow this logic along two complementary paths. First, using excitation tuned near the NV's zero-phonon line, we perform optically detected magnetic resonance (ODMR) spectroscopy at cryogenic temperatures in order to precisely measure the NV center's excited-state susceptibility to electric fields. In doing so, we demonstrate that the characteristically observed contrast inversion arises from an interplay between spin-selective optical pumping and the NV centers' local charge distribution. Second, motivated by this understanding, we propose and analyze a novel scheme for optically-enhanced electric-field sensing using NV ensembles; we estimate that our approach should enable order of magnitude improvements in the DC electric-field sensitivity.

Suppression of top-down influence decreases neuronal excitability and contrast sensitivity in the V1 cortex of cat

How top-down influence affects neuronal activity and information encoding in the primary visual cortex (V1) remains elusive. This study examined changes of neuronal excitability and contrast sensitivity in cat V1 cortex after top-down influence of area 7 (A7) was modulated by transcranial direct current stimulation (tDCS). The neuronal excitability in V1 cortex was evaluated by visually evoked field potentials (VEPs), and contrast sensitivity (CS) was assessed by the inverse of threshold contrast of neurons in response to visual stimuli at different performance accuracy. We found that the amplitude of VEPs in V1 cortex lowered after top-down influence suppression with cathode-tDCS in A7, whereas VEPs in V1 did not change after sham-tDCS in A7 and nonvisual cortical area 5 (A5) or cathode-tDCS in A5 and lesioned A7. Moreover, the mean CS of V1 neurons decreased after cathode-tDCS but not sham-tDCS in A7, which could recover after tDCS effect vanished. Comparisons of neuronal contrast-response functions showed that cathode-tDCS increased the stimulus contrast required to generate the half-maximum response, with a weakly-correlated reduction in maximum response but not baseline response. Therefore, top-down influence of A7 enhanced neuronal excitability in V1 cortex and improved neuronal contrast sensitivity by both contrast gain and response gain.

The diagnostic value of apparent diffusion coefficient to differentiate benign and malignant meningiomas

BACKGROUNDMeningiomas are the most common primary extra-axial non-glial intracranial tumors. The severe grade of meningioma, according to WHO, has the highest recurrence rate accompanied by high morbidity and mortality rates. Therefore, it is imperative to perform pre-operative assessments so the clinician can give prompt treatment to gain a better prognosis. It is a novel alternative way of predicting meningioma’s malignancy by calculating the tumor’s apparent diffusion coefficient (ADC) value. The objective of the study was to determine the value of ADC for differentiating benign and malignant meningiomas. METHODSThis cross-sectional study involved 32 subjects with clinically diagnosed or histologically verified meningioma (21 benign and 11 malignant). They underwent a head-magnetic resonance imaging (MRI) examination and biopsy. We calculated the ADC value by creating regions of interest (ROIs) on the solid part of the tumor, guided by contrast and fluid-attenuated inversion recovery (FLAIR) sequence. We analyzed the ADC value with independent t-test and Bland-Altman graphs, calculated the average difference, CI 95%, limit of agreement between observers, and ROC. RESULTSMean ADC of malignant meningiomas (0.877 ± 0.167 x 10-3 mm2/s) was significantly lower than that of benign meningiomas (0.990 ± 0.105 x 10-3 mm2/s) (p&lt;0.05). The ADC threshold is 0.886 x 10-3 mm2/s with sensitivity 63.6%, specificity 85.7%, positive predictive value 70% and negative predictive value 81.8%. CONCLUSIONThe ADC value measurement provides a discriminative feature to differentiate between benign and malignant meningiomas. However, the clinical applicability still needs to be elucidated, as histopathological confirmation remains the mainstay of definitive diagnosis.

Segmentation-Renormalized Deep Feature Modulation for Unpaired Image Harmonization.

Deep networks are now ubiquitous in large-scale multi-center imaging studies. However, the direct aggregation of images across sites is contraindicated for downstream statistical and deep learning-based image analysis due to inconsistent contrast, resolution, and noise. To this end, in the absence of paired data, variations of Cycle-consistent Generative Adversarial Networks have been used to harmonize image sets between a source and target domain. Importantly, these methods are prone to instability, contrast inversion, intractable manipulation of pathology, and steganographic mappings which limit their reliable adoption in real-world medical imaging. In this work, based on an underlying assumption that morphological shape is consistent across imaging sites, we propose a segmentation-renormalized image translation framework to reduce inter-scanner heterogeneity while preserving anatomical layout. We replace the affine transformations used in the normalization layers within generative networks with trainable scale and shift parameters conditioned on jointly learned anatomical segmentation embeddings to modulate features at every level of translation. We evaluate our methodologies against recent baselines across several imaging modalities (T1w MRI, FLAIR MRI, and OCT) on datasets with and without lesions. Segmentation-renormalization for translation GANs yields superior image harmonization as quantified by Inception distances, demonstrates improved downstream utility via post-hoc segmentation accuracy, and improved robustness to translation perturbation and self-adversarial attacks.

Dynamic Imaging of Nanostructures in an Electrolyte with a Scanning Electron Microscope.

The development of microfabricated liquid cells has enabled dynamic studies of nanostructures within a liquid environment with electron microscopy. While such setups are most commonly found in transmission electron microscope (TEM) holders, their implementation in a scanning electron microscope (SEM) offers intriguing potential for multi-modal studies where the large chamber volume allows for the integration of multiple detectors. Here, we describe an electrochemical liquid cell SEM platform that employs the same cells enclosed by silicon nitride membrane windows found in liquid cell TEM holders and demonstrate the imaging of copper oxide nanoparticles in solution using both backscattered and transmitted electrons. In particular, the transmitted electron images collected at high scattering angles show contrast inversion at liquid layer thicknesses of several hundred nanometers, which can be used to determine the presence of liquid in the cell, while maintaining enough resolution to image nanoparticles that are tens of nanometers in size. Using Monte Carlo simulations, we show that both imaging modes have their advantages for liquid phase imaging and rationalize the contrast inversion observed in the transmitted electron image.

Insight into the Charge Density Wave Gap from Contrast Inversion in Topographic STM Images.

Charge density waves (CDWs) are understood in great detail in one dimension, but they remain largely enigmatic in two-dimensional systems. In particular, numerous aspects of the associated energy gap and the formation mechanism are not fully understood. Two long-standing riddles are the amplitude and position of the CDW gap with respect to the Fermi level (E_{F}) and the frequent absence of CDW contrast inversion (CI) between opposite bias scanning tunneling microscopy (STM) images. Here, we find compelling evidence that these two issues are intimately related. Combining density functional theory and STM to analyze the CDW pattern and modulation amplitude in 1T-TiSe_{2}, we find that CI takes place at an unexpected negative sample bias because the CDW gap opens away from E_{F}, deep inside the valence band. This bias becomes increasingly negative as the CDW gap shifts to higher binding energy with electron doping. This study shows the importance of CI in STM images to identify periodic modulations with a CDW and to gain valuable insight into the CDW gap, whose measurement is notoriously controversial.