Image Acquisition Scheme Research Articles

Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits.

The automated tape-collecting ultramicrotome (ATUM) makes it possible to collect large numbers of ultrathin sections quickly—the equivalent of a petabyte of high resolution images each day. However, even high throughput image acquisition strategies generate images far more slowly (at present ~1 terabyte per day). We therefore developed WaferMapper, a software package that takes a multi-resolution approach to mapping and imaging select regions within a library of ultrathin sections. This automated method selects and directs imaging of corresponding regions within each section of an ultrathin section library (UTSL) that may contain many thousands of sections. Using WaferMapper, it is possible to map thousands of tissue sections at low resolution and target multiple points of interest for high resolution imaging based on anatomical landmarks. The program can also be used to expand previously imaged regions, acquire data under different imaging conditions, or re-image after additional tissue treatments.

A traverse inspection system for high precision visual on-loom fabric defect detection

A self-contained inspection system for vision-based on-loom fabric defect detection is presented in this paper. Design and loom integration of a traversing camera sled, a camera vibration damper and a complementary back-light illumination are presented and discussed. Image acquisition strategies and traverse control are described to complete the discussion on hardware and mechanics. The main part of the paper focuses on a novel algorithmic framework for woven fabric defect detection in highly resolved (1,000+ ppi) image data. Within this scope, single yarns are tracked and measured in terms of position, size, and appearance in real time. An inspection prototype has been mounted onto an industrial loom. Extensive on-line and off-line evaluations for various fabric materials gave precise and stable detection results with few false alarms. A brief cost analysis for the prototype system is provided and completes the presentation of the system.

The importance of image quality: In the eyes of the beholder?

The importance of image quality: In the eyes of the beholder?

Cardiac T 1 Imaging

T(1) mapping of the heart has evolved into a valuable tool to evaluate myocardial tissue properties, with or without contrast injection, including assessment of myocardial edema and free water content, extracellular volume (expansion), and most recently cardiomyocyte hypertrophy. The magnetic resonance imaging pulse sequence techniques developed for these applications have had to address at least 2 important considerations for cardiac applications: measure magnetization-inversion recoveries during cardiac motion with sufficient temporal resolution for the shortest expected T(1) values, and, second, obtain these measurements within a time during which a patient can comfortably suspend breathing. So-called Look-Locker techniques, and variants thereof, which all sample multiple points of a magnetization recovery after each magnetization preparation, have therefore become a mainstay in this field. The rapid pace of advances and new findings based on cardiac T(1) mapping for assessment of diffuse fibrosis or myocardial edema show that these techniques enrich the capabilities of magnetic resonance imaging for myocardial tissue profiling, which is arguably unmatched by other cardiac imaging modalities.

MRXCAT: Realistic numerical phantoms for cardiovascular magnetic resonance

Computer simulations are important for validating novel image acquisition and reconstruction strategies. In cardiovascular magnetic resonance (CMR), numerical simulations need to combine anatomical information and the effects of cardiac and/or respiratory motion. To this end, a framework for realistic CMR simulations is proposed and its use for image reconstruction from undersampled data is demonstrated. The extended Cardiac-Torso (XCAT) anatomical phantom framework with various motion options was used as a basis for the numerical phantoms. Different tissue, dynamic contrast and signal models, multiple receiver coils and noise are simulated. Arbitrary trajectories and undersampled acquisition can be selected. The utility of the framework is demonstrated for accelerated cine and first-pass myocardial perfusion imaging using k-t PCA and k-t SPARSE. MRXCAT phantoms allow for realistic simulation of CMR including optional cardiac and respiratory motion. Example reconstructions from simulated undersampled k-t parallel imaging demonstrate the feasibility of simulated acquisition and reconstruction using the presented framework. Myocardial blood flow assessment from simulated myocardial perfusion images highlights the suitability of MRXCAT for quantitative post-processing simulation. The proposed MRXCAT phantom framework enables versatile and realistic simulations of CMR including breathhold and free-breathing acquisitions.

Focus on software and data acquisition

Focus on software and data acquisition

Differential interferometry techniques on l-band data employed for the monitoring of surface subsidence due to mining

Mining activities in South Africa changes the natural environment in several ways. Challenges for mining companies lie in the detection and monitoring of surface subsidence and there exists a need for a long term monitoring system. Field-based techniques for deformation measurement are labour intensive and time consuming and, consequently, the implementation of these techniques for long-term monitoring is not ideal. On the other hand, satellite remote sensing data provides a synoptic view of an area and the repeat image acquisition strategy implies that the long-term monitoring of surface deformation is a possibility. This paper investigates the use of L-band ALOS PALSAR data for the detection and monitoring of surface subsidence due to underground mining activities in the Witbank Coalfields. Surface subsidence was detected for a period of over 3 years between 2007/08/16 and 2010/10/09. Centimetre scale surface deformation was detected in the study area and is associated with areas of active mining. The systematic evolution of the surface deformation basins over time was recognised and is consistent with the advance of the working face of the mine during the same period. The results confirm that L-band synthetic aperture radar data through dInSAR techniques can be used for the long-term monitoring of surface subsidence associated with mining activities.

The potential for Bayesian compressive sensing to significantly reduce electron dose in high-resolution STEM images

The use of high-resolution imaging methods in scanning transmission electron microscopy (STEM) is limited in many cases by the sensitivity of the sample to the beam and the onset of electron beam damage (for example, in the study of organic systems, in tomography and during in situ experiments). To demonstrate that alternative strategies for image acquisition can help alleviate this beam damage issue, here we apply compressive sensing via Bayesian dictionary learning to high-resolution STEM images. These computational algorithms have been applied to a set of images with a reduced number of sampled pixels in the image. For a reduction in the number of pixels down to 5% of the original image, the algorithms can recover the original image from the reduced data set. We show that this approach is valid for both atomic-resolution images and nanometer-resolution studies, such as those that might be used in tomography datasets, by applying the method to images of strontium titanate and zeolites. As STEM images are acquired pixel by pixel while the beam is scanned over the surface of the sample, these postacquisition manipulations of the images can, in principle, be directly implemented as a low-dose acquisition method with no change in the electron optics or the alignment of the microscope itself.

Visualization of intra-thalamic nuclei with optimized white-matter-nulled MPRAGE at 7 T

Novel MR image acquisition strategies have been investigated to elicit contrast within the thalamus, but direct visualization of individual thalamic nuclei remains a challenge because of their small size and the low intrinsic contrast between adjacent nuclei. We present a step-by-step specific optimization of the 3D MPRAGE pulse sequence at 7T to visualize the intra-thalamic nuclei. We first measured T1 values within different sub-regions of the thalamus at 7T in 5 individuals. We used these to perform simulations and sequential experimental measurements (n=17) to tune the parameters of the MPRAGE sequence. The optimal set of parameters was used to collect high-quality data in 6 additional volunteers. Delineation of thalamic nuclei was performed twice by one rater and MR-defined nuclei were compared to the classic Morel histological atlas. T1 values within the thalamus ranged from 1400ms to 1800ms for adjacent nuclei. Using these values for theoretical evaluations combined with in vivo measurements, we showed that a short inversion time (TI) close to the white matter null regime (TI=670ms) enhanced the contrast between the thalamus and the surrounding tissues, and best revealed intra-thalamic contrast. At this particular nulling regime, lengthening the time between successive inversion pulses (TS=6000ms) increased the thalamic signal and contrast and lengthening the α pulse train time (N*TR) further increased the thalamic signal. Finally, a low flip angle during the gradient echo acquisition (α=4°) was observed to mitigate the blur induced by the evolution of the magnetization along the α pulse train. This optimized set of parameters enabled the 3D delineation of 15 substructures in all 6 individuals; these substructures corresponded well with the known anatomical structures of the thalamus based on the classic Morel atlas. The mean Euclidean distance between the centers of mass of MR- and Morel atlas-defined nuclei was 2.67mm (±1.02mm). The reproducibility of the MR-defined nuclei was excellent with intraclass correlation coefficient measured at 0.997 and a mean Euclidean distance between corresponding centers of mass found at first versus second readings of 0.69mm (±0.38mm). This 7T strategy paves the way to better identification of thalamic nuclei for neurosurgical planning and investigation of regional changes in neurological disorders.

MRI Acquisition and Analysis Protocol for In Vivo Intraorbital Optic Nerve Segmentation at 3T

To present a new acquisition and analysis protocol for reliable and reproducible segmentation of the entire intraorbital optic nerve (ION) mean cross-sectional area by means of magnetic resonance imaging (MRI) at 3 tesla (T). Eight healthy volunteers (mean age 31, five were male) gave written informed consent and both of their IONs were imaged individually using a coronal-oblique T2-weighted fast multidynamic image acquisition scheme; the proposed acquisition scheme has its rationale in combining separately acquired volumes and registering them to account for motion-related artifacts commonly associated with longer acquisitions. Mean cross-sectional area of each ION was measured using a semiautomated image analysis protocol that was based on an active surface model previously described and used for spinal cord imaging. Reproducibility was assessed for repeated scans (scan-rescan) and repeated image analysis performance (intraobserver). Mean and SD values of the left ION cross-sectional area for the eight healthy volunteers were 5.0 (±0.7) mm² and for the right ION were 5.3 (±0.8) mm². Mean scan-rescan coefficient of variation (COV) for the left ION was 4.3% and for the right was 4.4%. Mean intraobserver COV for the left ION was 2.1% and for the right was 1.8%. This study presents a new MRI acquisition and analysis protocol for reliable and reproducible in vivo measurement of the entire ION mean cross-sectional area as demonstrated in a pilot study of healthy subjects. The protocol presented here can be used in future studies of the ION in disease state.

TH‐E‐103‐01: Nanotechnology & Molecular Imaging

TH‐E‐103‐01: Nanotechnology & Molecular Imaging

Image Quality and Radiation Dose Stratified by Patient Heart Rate for Coronary 64- and 320-MDCT Angiography

OBJECTIVE. The purpose of this study is to retrospectively measure and compare estimated radiation doses between consecutive patient cohorts who underwent coronary imaging CT with 64- and 320-MDCT scanners. MATERIALS AND METHODS. Subjects without arrhythmia (n = 4475) underwent imaging with 64-MDCT (n = 770) and 320-MDCT (n = 3705) scanners and were classified into one of five subgroups according to the patient heart rate and the image acquisition strategy. For all patients, image quality was subjectively evaluated using a 3-point scale. Estimated radiation dose and image quality were compared between subjects stratified by CT scanner and by subgroups imaged with each technology. RESULTS. For patients with a heart rate of 60 beats/min or less, the estimated radiation dose was halved (3.8 ± 2.0 vs 7.6 ± 2.6 mSv) when the 320-MDCT scanner (n = 2787) replaced the 64-MDCT scanner (n = 511). For the entire cohort, image quality score was significantly better (2.9 ± 0.4 vs 2.8 ± 0.5; p < 0.0001) and the effective dose was significantly lower (4.9 ± 3.3 vs 9.9 ± 5.4 mSv; p < 0.0001) for 320-MDCT scanners, compared with 64-MDCT scanners. CONCLUSION. Wide area-detector coronary CT angiography protocols have reduced radiation dose, with image quality maintained at the same level, compared with 64-MDCT technologies.

Monitoring Bone Marrow Stem Cells with a Reporter Gene System in Experimental Middle Cerebral Artery Occlusion Rat Models

This study was designed to investigate the feasibility of imaging bone marrow stem cells (BMSCs) in experimental middle cerebral artery occlusion (MCAO) rat models with a reporter gene-probe system, HSV1-tk-(131)I-2'-fluoro-2'-deoxy-1-β-d-arabinofuranosyl-5-iodouracil ((131)I-FIAU), and to choose the best strategies for stem cell injection, image acquisition, and imaging in vivo. A recombinant adenovirus (Ad5-TIBE) carrying the herpes simplex virus type 1 thymidine kinase (TK) reporter gene (HSV1-tk) linked via the internal ribosome entry site to the brain-derived neurotrophic factor therapeutic gene was prepared. After transfection with Ad5-TIBE, BMSCs were introduced into MCAO rat models via local injection into the brain or via injection into the lateral ventricle, carotid artery, and tail vein. Normal rats were used as controls. Twenty-four hours after (131)I-FIAU injection, rats were sacrificed for biodistribution analysis. The expression of the TK gene was evaluated by real-time quantitative polymerase chain reaction and Western blot analysis. Autoradiography was used for ex vivo imaging. SPECT images were obtained in MCAO rat models. The percentage injected dose per gram (%ID/g) in infarcted brain tissue in rats receiving the injection into the brain was 0.124 ± 0.013; this value was significantly higher than those in rats receiving the injection into the ventricle (0.052 ± 0.004), carotid artery (0.061 ± 0.002), and tail vein (0.059 ± 0.005) as well as normal rats (0.005 ± 0.001). No differences were seen in the other cell transplantation groups. The %ID/g in infarcted brain tissue was higher than that in the contralateral brain tissue in all experimental rats but not in normal rats. The expression of the TK gene in rats receiving a local injection into the brain was superior to that in all of the other groups. TK messenger RNA and protein expression showed a positive correlation with the %ID/g in brain tissue. Greater radioactivity at the injection site than in the surrounding and contralateral brain tissues in all experimental rats was indicated through autoradiography. The ratio of counts in bilateral brain tissues reached its peak (6.63) 24 h after (131)I-FIAU injection. SPECT images showed that radioactivity accumulation in the brain was low but increased gradually over time. The HSV1-tk-(131)I-FIAU reporter gene-probe system may be used to monitor BMSC activity in experimental MCAO rat models. Local injection of stem cells may provide an optimal means for cell transplantation, and imaging with (131)I-FIAU 24 h after injection provides peak target-to-nontarget count ratios.

Cardiovascular MR function and coronaries: CMR 15 minute express

Background CMR imaging has become a recognized gold-standard diagnostic technique for evaluating cardiovascular function, but has limited success in developing coronary imaging as a screening tool. With the faster image acquisition and reconstruction schemes, CMR can now be utilized as a non-invasive and robust screening modality of cardiovascular function and coronary disease in only 15 minutes of scanning. The 15 Minute Express Screening will enable further CMR imaging while maintaining a reasonable study length. To develop a high image-quality, repeatable, robust, and rapid clinical CMR diagnostic screening workflow, shorter than 15min, for cardiovascular function and coronary arteries.

Ensemble Analysis of Angiogenic Growth in Three-Dimensional Microfluidic Cell Cultures

We demonstrate ensemble three-dimensional cell cultures and quantitative analysis of angiogenic growth from uniform endothelial monolayers. Our approach combines two key elements: a micro-fluidic assay that enables parallelized angiogenic growth instances subject to common extracellular conditions, and an automated image acquisition and processing scheme enabling high-throughput, unbiased quantification of angiogenic growth. Because of the increased throughput of the assay in comparison to existing three-dimensional morphogenic assays, statistical properties of angiogenic growth can be reliably estimated. We used the assay to evaluate the combined effects of vascular endothelial growth factor (VEGF) and the signaling lipid sphingoshine-1-phosphate (S1P). Our results show the importance of S1P in amplifying the angiogenic response in the presence of VEGF gradients. Furthermore, the application of S1P with VEGF gradients resulted in angiogenic sprouts with higher aspect ratio than S1P with background levels of VEGF, despite reduced total migratory activity. This implies a synergistic effect between the growth factors in promoting angiogenic activity. Finally, the variance in the computed angiogenic metrics (as measured by ensemble standard deviation) was found to increase linearly with the ensemble mean. This finding is consistent with stochastic agent-based mathematical models of angiogenesis that represent angiogenic growth as a series of independent stochastic cell-level decisions.

Methodology for Reconstructing Early Zebrafish Development From In Vivo Multiphoton Microscopy

Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.

The missing link: do cortical microtubules define plasma membrane nanodomains that modulate cellulose biosynthesis?

Cellulose production is a crucial aspect of plant growth and development. It is functionally linked to cortical microtubules, which self-organize into highly ordered arrays often situated in close proximity to plasma membrane-bound cellulose synthase complexes (CSCs). Although most models put forward to explain the microtubule-cellulose relationship have considered mechanisms by which cortical microtubule arrays influence the orientation of cellulose microfibrils, little attention has been paid to how microtubules affect the physicochemical properties of cellulose. A recent study using the model system Arabidopsis, however, indicates that microtubules can modulate the crystalline and amorphous content of cellulose microfibrils. Microtubules are required during rapid growth for reducing crystalline content, which is predicted to increase the degree to which cellulose is tethered by hemicellulosic polysaccharides. Such tethering is, in turn, critical for maintaining unidirectional cell expansion. In this article, we hypothesize that cortical microtubules influence the crystalline content of cellulose either by controlling plasma membrane fluidity or by modulating the deposition of noncellulosic wall components in the vicinity of the CSCs. We discuss the current limitations of imaging technology to address these hypotheses and identify the image acquisition and processing strategies that will integrate live imaging with super resolution three-dimensional information.

Modeling non‐stationarity of kernel weights for k‐space reconstruction in partially parallel imaging

In partially parallel imaging, most k-space-based reconstruction algorithms such as GRAPPA adopt a single finite-size kernel to approximate the true relationship between sampled and nonsampled signals. However, the estimation of this kernel based on k-space signals is imperfect, and the authors are investigating methods dealing with local variation of k-space signals. To model nonstationarity of kernel weights, similar to performing a spatially adaptive regularization, the authors fit a set of linear functions using concepts from geographically weighted regression, a methodology used in geophysical analysis. Instead of a reconstruction with a single set of kernel weights, the authors use multiple sets. A missing signal is reconstructed with its kernel weights set determined by k-space clustering. Simulated and acquired MR data with several different image content and acquisition schemes, including MR tagging, were tested. A perceptual difference model (Case-PDM) was used to quantitatively evaluate the quality of over 1000 test images, and to optimize the parameters of our algorithm. A MOdeling Non-stationarity of KErnel wEightS ("MONKEES") reconstruction with two sets of kernel weights gave reconstructions with significantly better image quality than the original GRAPPA in all test images. Using more sets produced improved image quality but with diminishing returns. As a rule of thumb, at least two sets of kernel weights, one from low- and the other from high frequency k-space, should be used. The authors conclude that the MONKEES can significantly and robustly improve the image quality in parallel MR imaging, particularly, cardiac imaging.

Monitoring Rice Agriculture in the Sacramento Valley, USA With Multitemporal PALSAR and MODIS Imagery

Rice agriculture is an important crop that influences land-atmosphere interactions and requires substantial resources for flood management. Multitemporal acquisition strategies provide an opportunity to improve rice mapping and monitoring of hydroperiod. The objectives of this study were to 1) delineate rice paddies with Phased Array L-band Synthetic Aperture Radar (PALSAR) fine-beam single/dual (FBS/D) mode measurements and 2) integrate multitemporal, ScanSAR Wide-Beam 1 (WB1)- and Moderate Resolution Imaging Spectroradiometer (MODIS)- observations for flood frequency mapping. Multitemporal and multiscale PALSAR and MODIS imagery were collected over the study region in the Sacramento Valley, California, USA. A decision-tree approach utilized multitemporal FBS (HH polarization) data to classify rice fields and WB1 measurements to assess paddy flood status. High temporal frequency MODIS products further characterized hydroperiod for each individual rice paddy using a relationship between the Enhanced Vegetation Index (EVI) and the Land Surface Water Index (LSWI). Validation found the PALSAR-derived rice paddy extent maps and hydroperiod products to possess very high overall accuracies (95% overall accuracy). Agreement between MODIS and PALSAR flood products was strong with agreement between 85-94% at four comparison dates. By using complementing products and the strengths of each instrument, image acquisition strategies and monitoring protocol can be enhanced. The results highlight how the integration of multitemporal PALSAR and MODIS can be used to generate valuable agro-ecological information products in an operational context.

Pulmonary Kinematics From Image Data: A Review

The effects of certain lung pathologies include alterations in lung physiology negatively affecting pulmonary compliance. Current approaches to diagnosis and treatment assessment of lung disease commonly rely on pulmonary function testing. Such testing is limited to global measures of lung function, neglecting regional measurements, which are critical for early diagnosis and localization of disease. Increased accessibility to medical image acquisition strategies with high spatiotemporal resolution coupled with the development of sophisticated intensity-based and geometric registration techniques has resulted in the recent exploration of modeling pulmonary motion for calculating local measures of deformation. In this review, the authors provide a broad overview of such research efforts for the estimation of pulmonary deformation. This includes discussion of various techniques, current trends in validation approaches, and the public availability of software and data resources.