Rapid Volumetric Imaging Research Articles

DEEP BV: A FULLY AUTOMATED SYSTEM FOR BRAIN VENTRICLE LOCALIZATION AND SEGMENTATION IN 3D ULTRASOUND IMAGES OF EMBRYONIC MICE.

Volumetric analysis of brain ventricle (BV) structure is a key tool in the study of central nervous system development in embryonic mice. High-frequency ultrasound (HFU) is the only non-invasive, real-time modality available for rapid volumetric imaging of embryos in utero. However, manual segmentation of the BV from HFU volumes is tedious, time-consuming, and requires specialized expertise. In this paper, we propose a novel deep learning based BV segmentation system for whole-body HFU images of mouse embryos. Our fully automated system consists of two modules: localization and segmentation. It first applies a volumetric convolutional neural network on a 3D sliding window over the entire volume to identify a 3D bounding box containing the entire BV. It then employs a fully convolutional network to segment the detected bounding box into BV and background. The system achieves a Dice Similarity Coefficient (DSC) of 0.8956 for BV segmentation on an unseen 111 HFU volume test set surpassing the previous state-of-the-art method (DSC of 0.7119) by a margin of 25%.

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples

BackgroundAdvances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination.ResultsTo address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality.ConclusionsThe reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.

Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging.

Versatile, sterically accessible imaging systems capable of in vivo rapid volumetric functional and structural imaging deep in the brain continue to be a limiting factor in neuroscience research. Towards overcoming this obstacle, we present integrated one- and two-photon scanned oblique plane illumination (SOPi, /sōpī/) microscopy which uses a single front-facing microscope objective to provide light-sheet scanning based rapid volumetric imaging capability at subcellular resolution. Our planar scan-mirror based optimized light-sheet architecture allows for non-distorted scanning of volume samples, simplifying accurate reconstruction of the imaged volume. Integration of both one-photon (1P) and two-photon (2P) light-sheet microscopy in the same system allows for easy selection between rapid volumetric imaging and higher resolution imaging in scattering media. Using SOPi, we demonstrate deep, large volume imaging capability inside scattering mouse brain sections and rapid imaging speeds up to 10 volumes per second in zebrafish larvae expressing genetically encoded fluorescent proteins GFP or GCaMP6s. SOPi's flexibility and steric access makes it adaptable for numerous imaging applications and broadly compatible with orthogonal techniques for actuating or interrogating neuronal structure and activity.

Beyond backscattering: optical neuroimaging by BRAD.

Optical coherence tomography (OCT) is a powerful technology for rapid volumetric imaging in biomedicine. The bright field imaging approach of conventional OCT systems is based on the detection of directly backscattered light, thereby waiving the wealth of information contained in the angular scattering distribution. Here we demonstrate that the unique features of few-mode fibers (FMF) enable simultaneous bright and dark field (BRAD) imaging for OCT. As backscattered light is picked up by the different modes of a FMF depending upon the angular scattering pattern, we obtain access to the directional scattering signatures of different tissues by decoupling illumination and detection paths. We exploit the distinct modal propagation properties of the FMF in concert with the long coherence lengths provided by modern wavelength-swept lasers to achieve multiplexing of the different modal responses into a combined OCT tomogram. We demonstrate BRAD sensing for distinguishing differently sized microparticles and showcase the performance of BRAD-OCT imaging with enhanced contrast for ex vivo tumorous tissue in glioblastoma and neuritic plaques in Alzheimer’s disease.

Rapid volumetric imaging with Bessel-Beam three-photon microscopy.

Owing to its tissue-penetration ability, multi-photon fluorescence microscopy allows for the high-resolution, non-invasive imaging of deep tissue in vivo; the recently developed three-photon microscopy (3PM) has extended the depth of high-resolution, non-invasive functional imaging of mouse brains to beyond 1.0 mm. However, the low repetition rate of femtosecond lasers that are normally used in 3PM limits the temporal resolution of point-scanning three-photon microscopy. To increase the volumetric imaging speed of 3PM, we propose a combination of an axially elongated needle-like Bessel-beam with three-photon excitation (3PE) to image biological samples with an extended depth of focus. We demonstrate the higher signal-to-background ratio (SBR) of the Bessel-beam 3PM compared to the two-photon version both theoretically and experimentally. Finally, we perform simultaneous calcium imaging of brain regions at different axial locations in live fruit flies and rapid volumetric imaging of neuronal structures in live mouse brains. These results highlight the unique advantage of conducting rapid volumetric imaging with a high SBR in the deep brain in vivo using scanning Bessel-3PM.

Rapid volumetric photoacoustic tomographic imaging with a Fabry-Perot ultrasound sensor depicts peripheral arteries and microvascular vasomotor responses to thermal stimuli

PurposeTo determine if a new photoacoustic imaging (PAI) system successfully depicts (1) peripheral arteries and (2) microvascular circulatory changes in response to thermal stimuli.MethodsFollowing ethical permission, 8 consenting subjects underwent PAI of the dorsalis pedis (DP) artery, and 13 completed PAI of the index fingertip. Finger images were obtained after immersion in warm (30-35 °C) or cold (10-15 °C) water to promote vasodilation or vasoconstriction. The PAI instrument used a Fabry-Perot interferometeric ultrasound sensor and a 30-Hz 750-nm pulsed excitation laser. Volumetric images were acquired through a 14 × 14 × 14-mm volume over 90 s. Images were evaluated subjectively and quantitatively to determine if PAI could depict cold-induced vasoconstriction. The full width at half maximum (FWHM) of resolvable vessels was measured.ResultsFingertip vessels were visible in all participants, with mean FWHM of 125 μm. Two radiologists used PAI to correctly identify vasoconstricted fingertip capillary beds with 100% accuracy (95% CI 77.2-100.0%, p < 0.001). The number of voxels exhibiting vascular signal was significantly smaller after cold water immersion (cold: 5263 voxels; warm: 363,470 voxels, p < 0.001). The DP artery was visible in 7/8 participants (87.5%).ConclusionPAI achieves rapid, volumetric, high-resolution imaging of peripheral limb vessels and the microvasculature and is responsive to vasomotor changes induced by thermal stimuli.Key points• Fabry-Perot interferometer-based photoacoustic imaging (PAI) generates volumetric, high-resolution images of the peripheral vasculature.• The system reliably detects thermally induced peripheral vasoconstriction (100% correct identification rate, p < 0.001).• Vessels measuring less than 100 μm in diameter can be depicted in vivo.

Golden‐ratio rotated stack‐of‐stars acquisition for improved volumetric MRI

To develop and evaluate an improved stack-of-stars radial sampling strategy for reducing streaking artifacts. The conventional stack-of-stars sampling strategy collects the same radial angle for every partition (slice) encoding. In an undersampled acquisition, such an aligned acquisition generates coherent aliasing patterns and introduces strong streaking artifacts. We show that by rotating the radial spokes in a golden-angle manner along the partition-encoding direction, the aliasing pattern is modified, resulting in improved image quality for gridding and more advanced reconstruction methods. Computer simulations were performed and phantom as well as in vivo images for three different applications were acquired. Simulation, phantom, and in vivo experiments confirmed that the proposed method was able to generate images with less streaking artifact and sharper structures based on undersampled acquisitions in comparison with the conventional aligned approach at the same acceleration factors. By combining parallel imaging and compressed sensing in the reconstruction, streaking artifacts were mostly removed with improved delineation of fine structures using the proposed strategy. We present a simple method to reduce streaking artifacts and improve image quality in 3D stack-of-stars acquisitions by re-arranging the radial spoke angles in the 3D partition direction, which can be used for rapid volumetric imaging. Magn Reson Med 78:2290-2298, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

Sexual Dimorphism of Maxillary Sinus: A Morphometric Analysis using Cone Beam Computed Tomography.

Age and sex determination in forensic sciences are primary components of any skeletal analysis. As most bones used for sex determination are recovered in incomplete state, it is often necessary to use bones that are recovered intact e.g., the maxillary sinus. Cone Beam Computed Tomography (CBCT) can provide precise information about complex anatomical structures, as it is characterized by rapid volumetric image acquisition with high resolution. The present study was designed to evaluate the size and volume of Maxillary Sinus (MS) in determining gender by CBCT. Bilateral maxillary sinus images (left and right) were acquired for 100 patients (50 females and 50 males) and different parameters (width, length, height, area, perimeter and volume) were measured and evaluated. Mean and standard deviation of both maxillary sinuses measurements were calculated and compared. The data was subjected to discriminative statistical analysis and analysed using unpaired t-test. Comparison between male and female groups showed statistically insignificant differences on both the right and left sides with respect to the maxillary sinus length, height, area, volume and perimeter. However, the female group showed statistically significant higher values for left side MS width (p=0.041) and left side MS width can be used to determine gender with an overall accuracy of 60%. The final result of discriminative analysis shows that the ability of the maxillary sinus to identify gender was 68% in males and 74% in females with an overall accuracy of 71%. Maxillary sinus width can be used as an aid in forensic anthropology for gender determination.

Statistical intensity variation analysis for rapid volumetric imaging of capillary network flux.

We present a novel optical coherence tomography (OCT)-based technique for rapid volumetric imaging of red blood cell (RBC) flux in capillary networks. Previously we reported that OCT can capture individual RBC passage within a capillary, where the OCT intensity signal at a voxel fluctuates when an RBC passes the voxel. Based on this finding, we defined a metric of statistical intensity variation (SIV) and validated that the mean SIV is proportional to the RBC flux [RBC/s] through simulations and measurements. From rapidly scanned volume data, we used Hessian matrix analysis to vectorize a segment path of each capillary and estimate its flux from the mean of the SIVs gathered along the path. Repeating this process led to a 3D flux map of the capillary network. The present technique enabled us to trace the RBC flux changes over hundreds of capillaries with a temporal resolution of ~1 s during functional activation.

Comparative study of mandibular linear measurements obtained by cone beam computed tomography and digital calipers.

Objectives: Cone beam computed tomography (CBCT) is an innovative dental of imaging system characterized by rapid volumetric imaging with patient exposure to a single dose of radiation. The present study was carried out to compare the linear measurements obtained with CBCT and digital caliper in 20 mandibles from human cadavers. Study design: A total of 4800 linear measurements were measured between different mandibular anatomical points with CBCT and digital caliper. The real measurements were defined as those obtained with the digital caliper. Posteriorly, the mandibles were scanned to obtain the CBCT images, with software-based measurements of the distances. Results: The measurements obtained with the digital caliper were greater. The CBCT technique underestimated distances greater than 100 mm. Conclusions: CBCT allows to obtain linear mandibular anatomical measurements equivalent to those obtained with digital caliper. The differences existing between both methods were clinically acceptable. Key words:Computed tomography, cone beam CT, accuracy, reliability, digital caliper.

Extended depth of field microscopy for rapid volumetric two-photon imaging

Two-photon fluorescence microscopy is an influential tool in biology, providing valuable information on the activity of cells deep inside the tissue. However, it is limited by its low speed for imaging volume samples. Here we present the design of a two-photon scanning microscope with an extended and adjustable depth of field, which improves the temporal resolution for sampling thick samples. Moreover, this method implies no loss of optical power and resolution, and can be easily integrated into most commercial laser-scanning microscopy systems. We demonstrate experimentally the gain in performance of the system by comparing volumetric scans of neuronal structures with a standard versus an extended depth of field system.

Reevaluation of T2-weighted fast field echo (T2FFE): application to rapid volumetric black-blood imaging

T₂-fast field echo (T2FFE) sequence is a rapid T₂-weighted steady state free precession sequence, but has not become a widely utilized MR-imaging strategy because of its low signal-to-noise ratio and high sensitivity to motion. These effects have seriously limited the clinical use of T2FFE and therefore T2FFE has not been used for routine clinical studies. Nevertheless, in this study, we have investigated the possibility of clinical application by re-optimization of the T2FFE on the current MRI systems. Our purpose in this study was to explore the sensitivity of T2FFE to flow spins using a flow phantom and a contrast optimization/comparison with 2D turbo spin-echo (TSE) T₂-weighted images, and to evaluate its feasibility in volunteers and patients. This study demonstrated that the T2FFE sequence achieves rapid 3D T₂-weighted black-blood imaging while minimizing the impact of motion using a low flip angle under the shortest repetition time and the shortest echo time conditions. Furthermore, 3D T2FFE with use of an optimal flip angle (30°-40°) can provide contrast equivalent to that of 2D TSE T₂-weighted images. This proposed T2FFE sequence might be promising for numerous clinical applications.

Extended coherence length megahertz FDML and its application for anterior segment imaging

We present a 1300 nm Fourier domain mode locked (FDML) laser for optical coherence tomography (OCT) that combines both, a high 1.6 MHz wavelength sweep rate and an ultra-long instantaneous coherence length for rapid volumetric deep field imaging. By reducing the dispersion in the fiber delay line of the FDML laser, the instantaneous coherence length and hence the available imaging range is approximately quadrupled compared to previously published MHz-FDML setups, the imaging speed is increased by a factor of 16 compared to previous extended coherence length results. We present a detailed characterization of the FDML laser performance. We demonstrate for the first time MHz-OCT imaging of the anterior segment of the human eye. The OCT system provides enough imaging depth to cover the whole range from the top surface of the cornea down to the crystalline lens.

Quantitative Evaluation of Transform Domains for Compressive Sampling-Based Recovery of Sparsely Sampled Volumetric OCT Images

Recently, compressive sampling has received significant attention as an emerging technique for rapid volumetric imaging. We have previously investigated volumetric optical coherence tomography (OCT) image acquisition using compressive sampling techniques and showed that it was possible to recover image volumes from a subset of sampled images. Our previous findings used the multidimensional wavelet transform as the domain of sparsification for recovering OCT image volumes. In this report, we analyzed and compared the potential and efficiency of three other image transforms to reconstruct the same volumetric OCT image. Two quantitative measures, the mean square error and the structural similarity index, were applied to compare the quality of the reconstructed volumetric images. We observed that fast Fourier transformation and wavelet both are capable of reconstructing OCT image volumes for the orthogonal sparse sampling masks used in this report, but with different merits.

Fast volumetric imaging of ethanol metabolism in rat liver with hyperpolarized [1‐13C]pyruvate

Rapid volumetric imaging of hyperpolarized (13) C compounds allows the real-time measurement of metabolic activity and can be useful in distinguishing between normal and diseased tissues. This work extends a fast two-dimensional undersampled spiral MRSI sequence to provide volumetric coverage, acquiring a 16 × 16 × 12 matrix with a nominal isotropic resolution of 5 mm in 4.5 s. The rapid acquisition enables a high temporal resolution for dynamic imaging. This dynamic three-dimensional MRSI method was used to investigate hyperpolarized [1-(13) C]pyruvate metabolism modulated by the administration of ethanol in rat liver. A significant increase in the pyruvate to lactate conversion was observed in the liver as a result of the greater availability of NADH (nicotinamide adenine dinucleotide, reduced form) from ethanol metabolism.

TU‐E‐110‐01: Inverse Geometry CT

Purpose: Computed tomographic imaging has made tremendous progress in recent decades but challenges remain, including dose efficiency and avoiding cone beam artifacts in rapid volumetric imaging. The goal of this research is to explore Inverse Geometry CT (IGCT) as a potential solution to these problems.Methods: Rather illuminating the entire object with a single source, IGCT uses a distributed array of sources, each illuminating a portion of the volume. Two approaches have been studied, one using a scanned anode source (SS‐IGCT) and another using an array of discrete sources each with its own electron emitter (MS‐IGCT). The sequential illumination of subvolumes allows a “virtual bowtie” wherein each source has its own optimized intensity as a function of angle. Results: Results show that distributed sources in the axial direction can readily control cone beam artifacts. A gantry‐based MS‐IGCT system has been built and initial images have been collected. Compared to a conventional system, the virtual bowtie concept can significantly reduce effective dose for the same image quality. A key challenge with IGCT is achieving high x‐ray statistics since only a fraction of the object is illuminating in any instant. Thus, the method is well suited to lower dose scanning. Conclusion: IGCT uses distributed x‐ray sources to ensure sufficient sampling and to sculpt the illuminating x‐ray field. Initial results are promising.Research sponsored by GE Healthcare.The learning objectives are to familiarize the audience with1. Principles of Inverse Geometry CT (IGCT)2. Advantages of IGCT3. Challenges and disadvantages of IGCT4. Progress in IGCT to‐date

Rapid Volumetric OCT Image Acquisition Using Compressive Sampling

Acquiring three dimensional image volumes with techniques such as Optical Coherence Tomography (OCT) relies on reconstructing the tissue layers based on reflection of light from tissue interfaces. One B-mode scan in an image is acquired by scanning and concatenating several A-mode scans, and several contiguous slices are acquired to assemble a full 3D image volume. In this work, we demonstrate how Compressive Sampling (CS) can be used to accurately reconstruct 3D OCT images with minimal quality degradation from a subset of the original image. The full 3D image is reconstructed from sparsely sampled data by exploiting the sparsity of the image in a carefully chosen transform domain. We use several sub-sampling schemes, recover the full 3D image using CS, and show that there is negligible effect on clinically relevant morphometric measurements of the optic nerve head in the recovered image. The potential outcome of this work is a significant reduction in OCT image acquisition time, with possible extensions to speeding up acquisition in other imaging modalities such as ultrasound and MRI.

Rapid volumetric angiography of cortical microvasculature with optical coherence tomography.

We describe methods and algorithms for rapid volumetric imaging of cortical vasculature with optical coherence tomography (OCT). By optimizing system design, scanning protocols, and algorithms for visualization of capillary flow, comprehensive imaging of the surface pial vasculature and capillary bed is performed in approximately 12 s. By imaging during hypercapnia and comparing with simultaneous CCD imaging, the sources of contrast of OCT angiography are investigated.

Non‐invasive determination of tissue thermal parameters from high intensity focused ultrasound treatment monitored by volumetric MRI thermometry

A method is proposed for estimating the perfusion rate, thermal diffusivity, and the absorption coefficient that influence the local temperature during high intensity focused ultrasound (HIFU) thermotherapy procedures. For this purpose, HIFU heating experiments (N = 100) were performed ex vivo on perfused porcine kidney (N = 5) under different flow conditions. The resulting spatio-temporal temperature variations were measured non-invasively by rapid volumetric MR-temperature imaging. The bio-heat transfer (BHT) model was adapted to describe the spatio-temporal evolution of tissue temperature in the cortex. Absorption and perfusion coefficients were determined by fitting the integrated thermal load (spatial integration of the thermal maps) curves in time with an analytical solution of the BHT equation proposed for single point HIFU heating. Thermal diffusivity was determined independently by analyzing the spatial spread of the temperature in time during the cooling period. Absorption coefficient and thermal diffusivity were found to be independent of flow, with mean and average values of 11.0 +/- 1.85 mm(3) x K x J(-1) and 0.172 +/- 0.003 mm(2) x s(-1), respectively. A linear dependence of the calculated perfusion rate with flow was observed with a slope of 9.20 +/- 0.75 mm(-3). The perfusion was found to act as a scaling term with respect to temperature but with no effect on the spatial spread of temperature which only depends on the thermal diffusivity. All results were in excellent agreement with the BHT model, indicating that this model is suitable to predict the evolution of temperature in perfused organs. This quantitative approach allows for determination of tissue thermal parameters with excellent precision (within 10%) and may thus help in quantifying the influence of perfusion during MR guided high intensity focused ultrasound (MRgHIFU).

A parallel implementation of 3D CT image reconstruction on the Cell Broadband Engine

AbstractCone‐beam X‐ray computed tomography (CT) is attracting increasing attention due to its applications in medicine, biomedical sciences, material engineering, and non‐destructive industrial evaluation. Rapid volumetric image reconstruction is highly desirable in all these fields for prompt visualization and analysis of complex structures of interest. However, in most applications, volumetric image reconstruction is still a very demanding computational task. The Cell Broadband Engine architecture (CBEA) is a novel microprocessor architecture designed to provide power‐efficient and cost‐effective high‐performance processing for some of the world's most demanding applications, including next generation game consoles. Applications that show special promise of benefiting from CBEA are medical imaging, security and surveillance, digital media, entertainment, communications, and certain scientific workloads. We believe that the CBEA is a good vehicle for processing 3D CT image reconstructions because it has the capability of reaching 200 Gfps. We implemented 3D CT image reconstruction on the CBEA. However, the programming scheme of the CBEA is different from single‐core architectures. To archive peak performance on the CBEA, coding optimizations are needed to exploit the unique features of the hardware. In this paper, we describe the parallelization of the 3D image reconstruction algorithm on the CBEA. The results show that the CBEA can achieve significant run time savings. Copyright © 2009 John Wiley &amp; Sons, Ltd.