High-resolution Quantitative Imaging Research Articles

Multiparameter imaging of calcium and abscisic acid and high-resolution quantitative calcium measurements using R-GECO1-mTurquoise in Arabidopsis.

Calcium signals occur in specific spatio-temporal patterns in response to various stimuli and are coordinated with, for example, hormonal signals, for physiological and developmental adaptations. Quantification of calcium together with other signalling molecules is required for correlative analyses and to decipher downstream calcium-decoding mechanisms. Simultaneous invivo imaging of calcium and abscisic acid has been performed here to investigate the interdependence of the respective signalling processes in Arabidopsis thaliana roots. Advanced ratiometric genetically encoded calcium indicators have been generated and invivo calcium calibration protocols were established to determine absolute calcium concentration changes in response to auxin and ATP. In roots, abscisic acid induced long-term basal calcium concentration increases, while auxin triggered rapid signals in the elongation zone. The advanced ratiometric calcium indicator R-GECO1-mTurquoise exhibited an increased calcium signal resolution compared to commonly used Förster resonance energy transfer-based indicators. Quantitative calcium measurements in Arabidopsis root tips using R-GECO1-mTurquoise revealed detailed maps of absolute calcium concentration changes in response to auxin and ATP. Calcium calibration protocols using R-GECO1-mTurquoise enabled high-resolution quantitative imaging of resting cytosolic calcium concentrations and their dynamic changes that revealed distinct hormonal and ATP responses in roots.

3D MR fingerprinting with accelerated stack-of-spirals and hybrid sliding-window and GRAPPA reconstruction

PurposeWhole-brain high-resolution quantitative imaging is extremely encoding intensive, and its rapid and robust acquisition remains a challenge. Here we present a 3D MR fingerprinting (MRF) acquisition with a hybrid sliding-window (SW) and GRAPPA reconstruction strategy to obtain high-resolution T1, T2 and proton density (PD) maps with whole brain coverage in a clinically feasible timeframe. Methods3D MRF data were acquired using a highly under-sampled stack-of-spirals trajectory with a steady-state precession (FISP) sequence. For data reconstruction, kx-ky under-sampling was mitigated using SW combination along the temporal axis. Non-uniform fast Fourier transform (NUFFT) was then applied to create Cartesian k-space data that are fully-sampled in the in-plane direction, and Cartesian GRAPPA was performed to resolve kz under-sampling to create an alias-free SW dataset. T1, T2 and PD maps were then obtained using dictionary matching. ResultsPhantom study demonstrated that the proposed 3D-MRF acquisition/reconstruction method is able to produce quantitative maps that are consistent with conventional quantification techniques. Retrospectively under-sampled in vivo acquisition revealed that SW + GRAPPA substantially improves quantification accuracy over the current state-of-the-art accelerated 3D MRF. Prospectively under-sampled in vivo study showed that whole brain T1, T2 and PD maps with 1 mm3 resolution could be obtained in 7.5 min. Conclusions3D MRF stack-of-spirals acquisition with hybrid SW + GRAPPA reconstruction may provide a feasible approach for rapid, high-resolution quantitative whole-brain imaging.

Quantitative DLA-based compressed sensing for T1-weighted acquisitions

High resolution Manganese Enhanced Magnetic Resonance Imaging (MEMRI), which uses manganese as a T1 contrast agent, has great potential for functional imaging of live neuronal tissue at single neuron scale. However, reaching high resolutions often requires long acquisition times which can lead to reduced image quality due to sample deterioration and hardware instability. Compressed Sensing (CS) techniques offer the opportunity to significantly reduce the imaging time. The purpose of this work is to test the feasibility of CS acquisitions based on Diffusion Limited Aggregation (DLA) sampling patterns for high resolution quantitative T1-weighted imaging. Fully encoded and DLA-CS T1-weighted images of Aplysia californica neural tissue were acquired on a 17.2T MRI system. The MR signal corresponding to single, identified neurons was quantified for both versions of the T1 weighted images. For a 50% undersampling, DLA-CS can accurately quantify signal intensities in T1-weighted acquisitions leading to only 1.37% differences when compared to the fully encoded data, with minimal impact on image spatial resolution. In addition, we compared the conventional polynomial undersampling scheme with the DLA and showed that, for the data at hand, the latter performs better. Depending on the image signal to noise ratio, higher undersampling ratios can be used to further reduce the acquisition time in MEMRI based functional studies of living tissues.

Quantitative Evaluation of Stomatal Cytoskeletal Patterns during the Activation of Immune Signaling in Arabidopsis thaliana.

Historically viewed as primarily functioning in the regulation of gas and water vapor exchange, it is now evident that stomata serve an important role in plant immunity. Indeed, in addition to classically defined functions related to cell architecture and movement, the actin cytoskeleton has emerged as a central component of the plant immune system, underpinning not only processes related to cell shape and movement, but also receptor activation and signaling. Using high resolution quantitative imaging techniques, the temporal and spatial changes in the actin microfilament array during diurnal cycling of stomatal guard cells has revealed a highly orchestrated transition from random arrays to ordered bundled filaments. While recent studies have demonstrated that plant stomata close in response to pathogen infection, an evaluation of stimulus-induced changes in actin cytoskeletal dynamics during immune activation in the guard cell, as well as the relationship of these changes to the function of the actin cytoskeleton and stomatal aperture, remains undefined. In the current study, we employed quantitative cell imaging and hierarchical clustering analyses to define the response of the guard cell actin cytoskeleton to pathogen infection and the elicitation of immune signaling. Using this approach, we demonstrate that stomatal-localized actin filaments respond rapidly, and specifically, to both bacterial phytopathogens and purified pathogen elicitors. Notably, we demonstrate that higher order temporal and spatial changes in the filament array show distinct patterns of organization during immune activation, and that changes in the naïve diurnal oscillations of guard cell actin filaments are perturbed by pathogens, and that these changes parallel pathogen-induced stomatal gating. The data presented herein demonstrate the application of a highly tractable and quantifiable method to assign transitions in actin filament organization to the activation of immune signaling in plants.

WE-FG-202-02: Exploration of High-Resolution Quantitative Ultrasonic Micro-Vascular Imaging for Early Assessment of Radiotherapy Tumor Response

Purpose: Currently, we cannot predict an individual patient's response to a given radiotherapy which normally is not detected for weeks to months post-treatment. As a result, precious time is wasted for patients with unresponsive tumors who could have switched to an alternative treatment much earlier. Presently, no early treatment response detection method exists that is effective, low-cost, non-invasive, and safe. We hypothesize that changes in tumor microvasculature predict tumor response to radiotherapy earlier than tumor volume changes. Recent radiobiology research suggests tumors undergo vascular remodeling in response to radiation well before manifesting changes in tumor volume. We propose monitoring tumor microvasculature post-radiation using Acoustic Angiography (AA), a novel ultrasound imaging modality developed and patented in-house. In this study, we investigate whether changes in tumor microvasculature, measured using AA, can be an early indicator of high-dose radiotherapy success, compared to changes in tumor volume. Methods: Fibrosarcoma xenograft tumor tissue was subcutaneously implanted into rodent flanks (N=10). Animal tumors (N=8) were irradiated with a single treatment of 15Gy using a clinical LINAC at 100SSD and 2×2cm field size. Two untreated rats were left as tumor controls. AA imaging was performed immediately posttreatment and every third day thereafter for 30 days, or until tumors disappeared. Tumor volumes and vascular densities were measured from anatomical b-mode ultrasound and AA images, respectively. Results: Statistical differences in vascular density between treatment responders and non-responders were observed on Day 10 (p=0.005), whereas statistical differences in tumor volume were not observed until Day 19 (p=0.02). Conclusions: Tumor vascularity differences may be observed substantially earlier than differences in tumor size. In addition, significant early increases in vascular density were observed in non-responding tumors. This data is consistent with a similar study we completed using the same tumor and animal models (N=10) at 20Gy. The project described was supported by the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through Grant Award Number UL1TR001111. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Radiomics in Precision Radiotherapy

Radiomics is a new area of research, which converts imaging data into high-resolution quantitative imaging features by applying the automatic high-throughput imaging-feature-extraction algorithm. With the development of data science, more and more attention has been paid to the non-invasive and quantitative method in precision radiotherapy all over the world. This paper will briefly introduce the concept of radiomics and its application in precision radiotherapy. Key words: Radiomics; Precision radiotherapy; Image; Feature

Full-waveform inversion of GPR data acquired between boreholes in Rustrel carbonates

Full waveform inversion (FWI) of seismic or Ground Penetrating Radar data provides high-resolution quantitative images of the constitutive parameters of the rock/soil which control seismic/GPR wave propagation. We developed a 2D inversion tool in the frequency domain adapted to the multi-parameter physics controlling GPR propagation in isotropic non dispersive media, i.e. dielectric permittivity and electrical conductivity. This inversion engine was previously tested using synthetic 2D data to mitigate the trade-off between the two parameter classes. In this paper, we present the required processing techniques and first inversion results obtained on a real GPR dataset acquired in carbonates with a cross-hole configuration. The presence of the 2 m diameter underground gallery at depth constitutes a nice target to test the robustness, efficiency and resolution of the inversion in such high-contrasts context. Starting from a time tomographic image for the dielectric permittivity and from a homogeneous conductivity, we show that FWI is efficient to retrieve high resolution images of dielectric permittivity but struggles with electrical conductivity. As a quality control, we compare real and synthetic radargrams computed from the tomography and final images, showing the efficiency of the process to reconstruct some events but also underlying some issues, particularly on large incidence angles amplitude traces.

Performance of simultaneous high temporal resolution quantitative perfusion imaging of bladder tumors and conventional multi-phase urography using a novel free-breathing continuously acquired radial compressed-sensing MRI sequence

PurposeTo investigate the feasibility of high temporal resolution quantitative perfusion imaging of bladder tumors performed simultaneously with conventional multi-phase MR urography (MRU) using a novel free-breathing continuously acquired radial MRI sequence with compressed-sensing reconstruction. Methods22 patients with bladder lesions underwent MRU using GRASP (Golden-angle RAdial Sparse Parallel) acquisition. Multi-phase contrast-enhanced abdominopelvic GRASP was performed during free-breathing (1.4×1.4×3.0mm3 voxel size; 3:44min acquisition). Two dynamic datasets were retrospectively reconstructed by combining different numbers of sequentially acquired spokes into each dynamic frame: 110 spokes per frame for 25-s temporal resolution (serving as conventional MRU for clinical interpretation) and 8 spokes per frame for 1.7-s resolution. Using 1.7-s resolution images, ROIs were placed within bladder lesions and normal bladder wall, a femoral artery arterial input function was generated, and the Generalized Kinetic Model was applied. ResultsBiopsy/cystectomy demonstrated 16 bladder tumors (13 stage≥T2, 3 stage≤T1) and 6 benign lesions. All lesions were well visualized using 25-s clinical multi-phase images. Using 1.7-s resolution images, Ktrans was significantly higher in tumors (0.38±0.24) than normal bladder (0.12±0.02=8, p<0.001) or benign lesions (0.15±0.04, p=0.033). Ratio between Ktrans of lesions and normal bladder was nearly double for tumors than benign lesions (4.3±3.4 vs. 2.2±1.6), and Ktrans was nearly double in stage≥T2 than stage≤T1 tumors (0.44±0.24 vs. 0.24±0.24), although these did not approach significance (p=0.180–0.209), possibly related to small sample size. ConclusionGRASP allows simultaneous quantitative high temporal resolution perfusion of bladder lesions during clinical MRU examinations using only one contrast injection and without additional scan time.

Neuroprotection by caloric restriction is associated with a distinct state of hippocampal energy metabolism linked to PGC-1alpha and GSK3beta

The hippocampus is critical for cognition and memory formation and is vulnerable to age-related atrophy and loss of function. These phenotypes are attenuated by caloric restriction (CR), a dietary intervention that delays aging. Here we show significant effects of aging and CR on hippocampal energy metabolism that implicate metabolic pathways in neuronal protection. Using high-resolution quantitative imaging, we detected significant regional differences in activity of the mitochondrial electron transport system (ETS) in mouse hippocampi. Mitochondrial activity was lower in aged mice, and the impact of age was region specific. Multi-photon laser scanning microscopy revealed age- and region-specific differences within the dentate gyrus (DG), where levels of autofluroescence of NAD derived metabolic cofactors declined and chemical properties were altered. There was a significant regional impact of age to decrease levels of PGC-1alpha, a master regulator of ETS gene expression. Rather than reversing the impact of age, we found CR induced a distinct metabolic state. Fluorescence intensity of NAD(P) H was higher in the DG of CR animals, but CR had no impact on fluorescence decay parameters. Levels of PGC-1alpha were lower with CR, as were levels of GSK3beta, a key regulator of PGC-1alpha turnover and activity, and these differences were conserved in rhesus monkeys. These data reveal significant changes in hippocampal energy metabolism with age and suggest CR’s prevention of age-related functional decline involves extensive metabolic reprogramming.

Active intracellular transport in metastatic cells studied by spatial light interference microscopy.

Spatiotemporal patterns of intracellular transport are very difficult to quantify and, consequently, continue to be insufficiently understood. While it is well documented that mass trafficking inside living cells consists of both random and deterministic motions, quantitative data over broad spatiotemporal scales are lacking. We studied the intracellular transport in live cells using spatial light interference microscopy, a high spatiotemporal resolution quantitative phase imaging tool. The results indicate that in the cytoplasm, the intracellular transport is mainly active (directed, deterministic), while inside the nucleus it is both active and passive (diffusive, random). Furthermore, we studied the behavior of the two-dimensional mass density over 30 h in HeLa cells and focused on the active component. We determined the standard deviation of the velocity distribution at the point of cell division for each cell and compared the standard deviation velocity inside the cytoplasm and the nucleus. We found that the velocity distribution in the cytoplasm is consistently broader than in the nucleus, suggesting mechanisms for faster transport in the cytosol versus the nucleus. Future studies will focus on improving phase measurements by applying a fluorescent tag to understand how particular proteins are transported inside the cell.

Improved quantitative phase imaging in lensless microscopy by single-shot multi-wavelength illumination using a fast convergence algorithm.

We report on a novel algorithm for high-resolution quantitative phase imaging in a new concept of lensless holographic microscope based on single-shot multi-wavelength illumination. This new microscope layout, reported by Noom et al. along the past year and named by us as MISHELF (initials incoming from Multi-Illumination Single-Holographic-Exposure Lensless Fresnel) microscopy, rises from the simultaneous illumination and recording of multiple diffraction patterns in the Fresnel domain. In combination with a novel and fast iterative phase retrieval algorithm, MISHELF microscopy is capable of high-resolution (micron range) phase-retrieved (twin image elimination) biological imaging of dynamic events. In this contribution, MISHELF microscopy is demonstrated through qualitative concept description, algorithm implementation, and experimental validation using both a synthetic object (resolution test target) and a biological sample (swine sperm sample) for the case of three (RGB) illumination wavelengths. The proposed method becomes in an alternative instrument improving the capabilities of existing lensless microscopes.

High-resolution quantitative imaging of the substantia nigra.

There is a growing interest in identifying neuroimaging-based biomarkers for Parkinson's disease (PD), a progressive neurodegenerative disorder in which the major pathologic substrate is the loss of pigmented dopaminergic neurons in the substantia nigra (SN). Recently, an MRI technique dubbed "neuromelanin-sensitive MRI" (NM-MRI), has been found to provide notable contrast between the SN and surrounding brain tissues with potential applications as biomarker of PD. The contrast in NM-MRI has been associated with magnetization transfer (MT) effects, and thus the goal of this study was to characterize the impact of MT on NM-MRI, and to demonstrate the feasibility of performing quantitative MT (qMT) imaging in human SN. The results of this study demonstrate that high-resolution rapid qMT imaging of the SN can be reliably obtained within reasonable scan times, thereby can be translatable into clinical practice.

Frequency domain ultrasound waveform tomography: breast imaging using a ring transducer

Application of the frequency domain acoustic wave equation on data acquired from ultrasound tomography scans is shown to yield high resolution sound speed images on the order of the wavelength of the highest reconstructed frequency. Using a signal bandwidth of 0.4–1 MHz and an average sound speed of 1500 m s−1, the resolution is approximately 1.5 mm. The quantitative sound speed values and morphology provided by these images have the potential to inform diagnosis and classification of breast disease. In this study, we present the formalism, practical application, and in vivo results of waveform tomography applied to breast data gathered by two different ultrasound tomography scanners that utilize ring transducers. The formalism includes a review of frequency domain modeling of the wave equation using finite difference operators as well as a review of the gradient descent method for the iterative reconstruction scheme. It is shown that the practical application of waveform tomography requires an accurate starting model, careful data processing, and a method to gradually incorporate higher frequency information into the sound speed reconstruction. Following these steps resulted in high resolution quantitative sound speed images of the breast. These images show marked improvement relative to commonly used ray tomography reconstruction methods. The robustness of the method is demonstrated by obtaining similar results from two different ultrasound tomography devices. We also compare our method to MRI to demonstrate concordant findings. The clinical data used in this work was obtained from a HIPAA compliant clinical study (IRB 040912M1F).

How adhesion forms the early mammalian embryo.

The early mouse embryo is an excellent system to study how a small group of initially rounded cells start to change shape and establish the first forms of adhesion-based cell-cell interactions in mammals in vivo. In addition to its critical role in the structural integrity of the embryo, we discuss here how adhesion is important to regulate cell polarity and cell fate. Recent evidence suggests that adherens junctions participate in signaling pathways by localizing key proteins to subcellular microdomains. E-cadherin has been identified as the main player required for the establishment of adhesion but other mechanisms involving additional proteins or physical forces acting in the embryo may also contribute. Application of new technologies that enable high-resolution quantitative imaging of adhesion protein dynamics and measurements of biomechanical forces will provide a greater understanding of how adhesion patterns the early mammalian embryo.

Quantitative imaging of selenoprotein with multi‐isotope imaging mass spectrometry (MIMS)

Multi-isotope imaging mass spectrometry (MIMS) allows high resolution quantitative imaging of protein and nucleic acid synthesis at the level of a single cell using stable isotope labels. We employed MIMS to determine the compartmental localization of selenoproteins tagged with stable isotope selenium compounds in human aortic endothelial cells (HAEC), and to compare the efficiency of labeling (to determine the ideal selenium source) from these compounds: [82Se]-selenite, [77Se]-seleno-methionine, and [76Se]-methyl-selenocysteine. We found that all three selenium sources appear to be localized in the nucleus as well as in the cytoplasm in HAEC. Seleno-methionine appears to be a better source for (seleno)protein synthesis. For MIMS detection, we compared freeze-drying to thin layer vs. thin sectioning for sample preparation. MIMS provides a unique and novel way to dissect selenoprotein synthesis in cells.

Fast Label-Free Cytoskeletal Network Imaging in Living Mammalian Cells

We present a full-field technique that allows label-free cytoskeletal network imaging inside living cells. This noninvasive technique allows monitoring of the cytoskeleton dynamics as well as interactions between the latter and organelles on any timescale. It is based on high-resolution quantitative phase imaging (modified Quadriwave lateral shearing interferometry) and can be directly implemented using any optical microscope without modification. We demonstrate the capability of our setup on fixed and living Chinese hamster ovary cells, showing the cytoskeleton dynamics in lamellipodia during protrusion and mitochondria displacement along the cytoskeletal network. In addition, using the quantitative function of the technique, along with simulation tools, we determined the refractive index of a single tubulin microtubule to be ntubu=2.36±0.6 at λ=527 nm.

High‐resolution quantitative sodium imaging at 9.4 tesla

Investigation of the feasibility to perform high-resolution quantitative sodium imaging at 9.4 Tesla (T). A proton patch antenna was combined with a sodium birdcage coil to provide a proton signal without compromising the efficiency of the X-nucleus coil. Sodium density weighted images with a nominal resolution of 1 × 1 × 5 mm(3) were acquired within 30 min with an ultrashort echo time sequence. The methods used for signal calibration as well as for B0, B1, and off-resonance correction were verified on a phantom and five healthy volunteers. An actual voxel volume of roughly 40 μL could be achieved at 9.4T, while maintaining an acceptable signal-to-noise ratio (8 for brain tissue and 35 for cerebrospinal fluid). The measured mean sodium concentrations for gray and white matter were 36 ± 2 and 31 ± 1 mmol/L of wet tissue, which are comparable to values previously reported in the literature. The reduction of partial volume effects is essential for accurate measurement of the sodium concentration in the human brain. Ultrahigh field imaging is a viable tool to achieve this goal due to its increased sensitivity.

High-resolution quantitative spiral perfusion for microvascular coronary dysfunction detection

Background Quantitative first-pass CMR can assess the severity of microvascular coronary dysfunction(MCD) in subjects with signs and symptoms of ischemia but without obstructive coronary artery disease(CAD). In patients with MCD, abnormalities of myocardial perfusion reserve (MPR) occur globally but may also vary in their transmural extent. Thus, high spatial resolution quantitative CMR perfusion imaging is needed to differentiate between the subendocardial and subepicardial layers. Given the efficiency and SNR of spiral trajectories, we have developed the accelerated high-resolution absolute

Quantitative cerebral blood flow imaging with extended-focus optical coherence microscopy

Quantitative three-dimensional blood flow imaging is a valuable technique to investigate the physiology of the brain. Two-photon microscopy (2PM) allows quantification of the local blood flow velocity with micrometric resolution by performing repeated line scans, but prohibitively long measurement times would be required to apply this technique to full three-dimensional volumes. By multiplexing the image acquisition over depth, Fourier domain optical coherence tomography (FDOCT) enables quantification of blood flow velocities with a high volume acquisition rate, albeit at a relatively low spatial resolution. Extended-focus optical coherence microscopy (xfOCM) increases the lateral resolution without sacrificing depth of field and therefore combines the high volume acquisition rate of FDOCT with a resolution comparable to 2PM. Here, we demonstrate high-resolution quantitative imaging of the blood flow velocity vector's magnitude in the adult murine brain with xfOCM.

High-resolution quantitative seismic imaging of a strike-slip fault with small vertical offset in clay rocks from underground galleries: Experimental platform of Tournemire, France

Imaging tectonic faults with small vertical offsets in argillites (clay rock) using geophysical methods is challenging. In the context of deep radioactive waste disposals, the presence of such faults has to be assessed because they can modify the rock-confining properties. In the Tournemire Experimental Platform (TEP, Aveyron, France), fault zones with small vertical offsets and complex shape have been identified from underground works. However, 3D high-resolution surface seismic methods have limitations in this context that led us to consider the detection and characterization of the faults directly from underground works. We investigated the potential of seismic full-waveform inversion (FWI) applied in a transmission configuration to image the clay rock medium in a horizontal plane between galleries and compared it with first-arrival traveltime tomography (FATT). Our objective was to characterize seismic velocities of a block of argillites crossed by a subvertical fault zone with a small vertical offset. The specific measurement configuration allowed us to neglect the influence of the galleries on the wave propagation and to simplify the problem by considering a 2D isotropic horizontal imaging domain. Our FWI scheme relied on a robust adaptation of early arrival waveform tomography. The results obtained with FATT and FWI were in accordance, and both correlated with the geologic observations from the gallery walls and boreholes. We found that even though various simplifications was done in the inversion scheme and only a part of the data was used, FWI allowed us to get higher resolution images than FATT, and it was especially less sensitive to the incomplete illumination because it also used diffracted energy. Our results highlighted the complexity of the fault zone, showing a complex interaction of the main fault system with a secondary system composed of decimetric fractures associated with the presence of water.