SLIME: robust, high-speed 3D microvascular mapping.
Ontology highlight
ABSTRACT:
SUBMITTER: Liu Y
PROVIDER: S-EPMC6351571 | biostudies-literature | 2019 Jan
REPOSITORIES: biostudies-literature
Publications
SLIME: robust, high-speed 3D microvascular mapping.
Liu Yehe Y Broberg Meredith C G MCG Watanabe Michiko M Rollins Andrew M AM Jenkins Michael W MW
Scientific reports 20190129 1
Three dimensional (3D) microvascular imaging of cubic millimeter to centimeter size volumes often requires much time and expensive instruments. By combining optical clearing with a novel scatter-based optical coherence tomography (OCT) contrast agent, we have greatly extended OCT imaging depth in excised tissues while maintaining a simple and low cost approach that does not require in-depth OCT knowledge. The new method enables fast 3D microvascular mapping in large tissue volumes, providing a p ...[more]
Similar Datasets
Project description:How genomic DNA is organized in the nucleus is a long-standing question. We describe a single-molecule bioimaging method utilizing super-localization precision coupled to fully quantitative image analysis tools, towards determining snapshots of parts of the 3D genome architecture of model eukaryote budding yeast Saccharomyces cerevisiae with exceptional millisecond time resolution. We employ astigmatism imaging to enable robust extraction of 3D position data on genomically encoded fluorescent protein reporters that bind to DNA. Our relatively straightforward method enables snippets of 3D architectures of likely single genome conformations to be resolved captured via DNA-sequence specific binding proteins in single functional living cells.
| S-EPMC6971689 | biostudies-literature
Project description:Noninvasive microvascular imaging using optical coherence Doppler tomography (ODT) has shown great promise in brain studies; however, high-speed microcirculatory imaging in deep brain remains an open quest. A high-speed 1.3 μm swept-source ODT (SS-ODT) system is reported which was based on a 200 kHz vertical-cavity-surface-emitting laser. Phase errors induced by sweep-trigger desynchronization were effectively reduced by spectral phase encoding and instantaneous correlation among the A-scans. Phantom studies have revealed a significant reduction in phase noise, thus an enhancement of minimally detectable flow down to 268.2 μm/s. Further in vivo validation was performed, in which 3D cerebral-blood-flow (CBF) networks in mouse brain over a large field-of-view (FOV: 8.5 × 5 × 3.2 mm3) was scanned through thinned skull. Results showed that fast flows up to 3 cm/s in pial vessels and minute flows down to 0.3 mm/s in arterioles or venules were readily detectable at depths down to 3.2 mm. Moreover, the dynamic changes of the CBF networks elicited by acute cocaine such as heterogeneous responses in various vessel compartments and at different cortical layers as well as transient ischemic events were tracked, suggesting the potential of SS-ODT for brain functional imaging that requires high flow sensitivity and dynamic range, fast frame rate and a large FOV to cover different brain regions.
| S-EPMC5146972 | biostudies-literature
Project description:Three-dimensional (3D) fluorescence imaging is important to accurately capture and understand biological structures and phenomena. However, because of its slow acquisition speed, it was difficult to implement 3D fluorescence imaging for imaging flow cytometry. Especially, modern flow cytometers operate at a flow velocity of 1-10 m/s, and no 3D fluorescence imaging technique was able to capture cells at such high velocity. Here, we present a high-speed 3D fluorescence imaging technique in which a set of optical cross sections of a cell is captured within a single frame of a camera by combining strobe light-sheet excitation and optofluidic spatial transformation. Using this technique, we demonstrated 3D fluorescence imaging of cells flowing at a velocity of over 10 m/s, which is the fastest to our knowledge. Such technology can allow integration of 3D imaging with flow systems of common flow cytometers and cell sorters.
| S-EPMC9208600 | biostudies-literature
Project description:PurposeQuantitative MRI applications, such as mapping the T1 time of tissue, puts high demands on the accuracy and precision of transmit field ( B1+ ) estimation. A candidate approach to satisfy these requirements exploits the difference in phase induced by the Bloch-Siegert frequency shift (BSS) of 2 acquisitions with opposite off-resonance frequency radiofrequency pulses. Interleaving these radiofrequency pulses ensures robustness to motion and scanner drifts; however, here we demonstrate that doing so also introduces a bias in the B1+ estimates.Theory and methodsIt is shown here by means of simulation and experiments that the amplitude of the error depends on MR pulse sequence parameters, such as repetition time and radiofrequency spoiling increment, but more problematically, on the intrinsic properties, T1 and T2 , of the investigated tissue. To solve these problems, a new approach to BSS-based B1+ estimation that uses a multi-echo acquisition and a general linear model to estimate the correct BSS-induced phase is presented.ResultsIn line with simulations, phantom and in vivo experiments confirmed that the general linear model-based method removed the dependency on tissue properties and pulse sequence settings.ConclusionThe general linear model-based method is recommended as a more accurate approach to BSS-based B1+ mapping.
| S-EPMC6771691 | biostudies-literature
Project description:Walking and running are mechanically and energetically different locomotion modes. For selecting one or another, speed is a parameter of paramount importance. Yet, both are likely controlled by similar low-dimensional neuronal networks that reflect in patterned muscle activations called muscle synergies. Here, we challenged human locomotion by having our participants walk and run at a very broad spectrum of submaximal and maximal speeds. The synergistic activations of lower limb locomotor muscles were obtained through decomposition of electromyographic data via non-negative matrix factorization. We analyzed the duration and complexity (via fractal analysis) over time of motor primitives, the temporal components of muscle synergies. We found that the motor control of high-speed locomotion was so challenging that the neuromotor system was forced to produce wider and less complex muscle activation patterns. The motor modules, or time-independent coefficients, were redistributed as locomotion speed changed. These outcomes show that humans cope with the challenges of high-speed locomotion by adapting the neuromotor dynamics through a set of strategies that allow for efficient creation and control of locomotion.
| S-EPMC7610320 | biostudies-literature
Project description:PurposeThe aim of this work is the reconciliation of high spatial and temporal resolution for MRI. For this purpose, a novel sampling strategy for 3D encoding is proposed, which provides flexible k-space segmentation along with uniform sampling density and benign filtering effects related to signal decay.MethodsFor time-critical MRI applications such as functional MRI (fMRI), 3D k-space is usually sampled by stacking together 2D trajectories such as echo planar imaging (EPI) or spiral readouts, where each shot covers one k-space plane. For very high temporal and medium to low spatial resolution, tilted hexagonal sampling (T-Hex) was recently proposed, which allows the acquisition of a larger k-space volume per excitation than can be covered with a planar readout. Here, T-Hex is described in a modified version where it instead acquires a smaller k-space volume per shot for use with medium temporal and high spatial resolution.ResultsMono-planar T-Hex sampling provides flexibility in the choice of speed, signal-to-noise ratio (SNR), and contrast for rapid MRI acquisitions. For use with a conventional gradient system, it offers the greatest benefit in a regime of high in-plane resolution <1 mm. The sampling scheme is combined with spirals for high sampling speed as well as with more conventional EPI trajectories.ConclusionMono-planar T-Hex sampling combines fast 3D encoding with SNR efficiency and favorable depiction characteristics regarding noise amplification and filtering effects from T2∗ decay, thereby providing flexibility in the choice of imaging parameters. It is attractive both for high-resolution time series such as fMRI and for applications that require rapid anatomical imaging.
| S-EPMC9292510 | biostudies-literature
Project description:We addressed the coating 5 mm-long cantilever microprobes with a viscoelastic material, which was intended to considerably extend the range of the traverse speed during the measurements of the 3D surface topography by damping contact-induced oscillations. The damping material was composed of epoxy glue, isopropyl alcohol, and glycerol, and its deposition onto the cantilever is described, as well as the tests of the completed cantilevers under free-oscillating conditions and in contact during scanning on a rough surface. The amplitude and phase of the cantilever's fundamental out-of-plane oscillation mode was investigated vs. the damping layer thickness, which was set via repeated coating steps. The resonance frequency and quality factor decreased with the increasing thickness of the damping layer for both the free-oscillating and in-contact scanning operation mode, as expected from viscoelastic theory. A very low storage modulus of E'≈100kPa, a loss modulus of E″≈434kPa, and a density of ρ≈1.2gcm-3 were yielded for the damping composite. Almost critical damping was observed with an approximately 130 µm-thick damping layer in the free-oscillating case, which was effective at suppressing the ringing behavior during the high-speed in-contact probing of the rough surface topography.
| S-EPMC9967852 | biostudies-literature
Project description:PurposeTo achieve motion robust high resolution 3D free-breathing pulmonary MRI utilizing a novel dynamic 3D image navigator derived directly from imaging data.MethodsFive-minute free-breathing scans were acquired with a 3D ultrashort echo time (UTE) sequence with 1.25 mm isotropic resolution. From this data, dynamic 3D self-navigating images were reconstructed under locally low rank (LLR) constraints and used for motion compensation with one of two methods: a soft-gating technique to penalize the respiratory motion induced data inconsistency, and a respiratory motion-resolved technique to provide images of all respiratory motion states.ResultsRespiratory motion estimation derived from the proposed dynamic 3D self-navigator of 7.5 mm isotropic reconstruction resolution and a temporal resolution of 300 ms was successful for estimating complex respiratory motion patterns. This estimation improved image quality compared to respiratory belt and DC-based navigators. Respiratory motion compensation with soft-gating and respiratory motion-resolved techniques provided good image quality from highly undersampled data in volunteers and clinical patients.ConclusionAn optimized 3D UTE sequence combined with the proposed reconstruction methods can provide high-resolution motion robust pulmonary MRI. Feasibility was shown in patients who had irregular breathing patterns in which our approach could depict clinically relevant pulmonary pathologies. Magn Reson Med 79:2954-2967, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
| S-EPMC6474413 | biostudies-literature
Project description:Digital holography allows production of high-speed three-dimensional images at rates over 100,000 frames per second; however, simultaneously obtaining suitable performance and levels of accuracy using digital holography is difficult. This problem prevents high-speed three-dimensional imaging from being used for vibrometry. In this paper, we propose and test a digital holography method that can produce vibration measurements. The method is based on single-shot phase-shifting interferometry. Herein, we imaged the surface of a loudspeaker diaphragm and measured its displacement due to the vibrations produced by a frequency sweep signal. We then analyzed the frequency of the experimental data and confirmed that the frequency spectra inferred from the reconstructed images agreed well with the spectra produced by the sound recorded by a microphone. This method can be used for measuring vibrations with three-dimensional imaging for loudspeakers, microelectromechanical systems, surface acoustic wave filters, and biological tissues and organs.
| S-EPMC5585211 | biostudies-literature
Project description:BACKGROUND:Cardiovascular magnetic resonance (CMR) T1? mapping can be used to detect ischemic or non-ischemic cardiomyopathy without the need of exogenous contrast agents. Current 2D myocardial T1? mapping requires multiple breath-holds and provides limited coverage. Respiratory gating by diaphragmatic navigation has recently been exploited to enable free-breathing 3D T1? mapping, which, however, has low acquisition efficiency and may result in unpredictable and long scan times. This study aims to develop a fast respiratory motion-compensated 3D whole-heart myocardial T1? mapping technique with high spatial resolution and predictable scan time. METHODS:The proposed electrocardiogram (ECG)-triggered T1? mapping sequence is performed under free-breathing using an undersampled variable-density 3D Cartesian sampling with spiral-like order. Preparation pulses with different T1? spin-lock times are employed to acquire multiple T1?-weighted images. A saturation prepulse is played at the start of each heartbeat to reset the magnetization before T1? preparation. Image navigators are employed to enable beat-to-beat 2D translational respiratory motion correction of the heart for each T1?-weighted dataset, after which, 3D translational registration is performed to align all T1?-weighted volumes. Undersampled reconstruction is performed using a multi-contrast 3D patch-based low-rank algorithm. The accuracy of the proposed technique was tested in phantoms and in vivo in 11 healthy subjects in comparison with 2D T1? mapping. The feasibility of the proposed technique was further investigated in 3 patients with suspected cardiovascular disease. Breath-hold late-gadolinium enhanced (LGE) images were acquired in patients as reference for scar detection. RESULTS:Phantoms results revealed that the proposed technique provided accurate T1? values over a wide range of simulated heart rates in comparison to a 2D T1? mapping reference. Homogeneous 3D T1? maps were obtained for healthy subjects, with septal T1? of 58.0 ± 4.1?ms which was comparable to 2D breath-hold measurements (57.6 ± 4.7?ms, P?=?0.83). Myocardial scar was detected in 1 of the 3 patients, and increased T1? values (87.4 ± 5.7?ms) were observed in the infarcted region. CONCLUSIONS:An accelerated free-breathing 3D whole-heart T1? mapping technique was developed with high respiratory scan efficiency and near-isotropic spatial resolution (1.7 × 1.7 × 2?mm3) in a clinically feasible scan time of ~?6 mins. Preliminary patient results suggest that the proposed technique may find applications in non-contrast myocardial tissue characterization.
| S-EPMC6998259 | biostudies-literature