scholarly journals A critical assessment of data quality and venous effects in ultra-high-resolution fMRI

2018 ◽  
Author(s):  
Kendrick Kay ◽  
Keith W. Jamison ◽  
Luca Vizioli ◽  
Ruyuan Zhang ◽  
Eshed Margalit ◽  
...  
Keyword(s):  
High Resolution ◽  
Signal To Noise Ratio ◽  
Activity Patterns ◽  
Sampling Rate ◽  
Pulse Sequences ◽  
Blood Oxygenation ◽  
Fine Scale ◽  
Cortical Folding ◽  
Neuroscience Research ◽  
Spatial Coverage

AbstractAdvances in hardware, pulse sequences, and reconstruction techniques have made it possible to perform functional magnetic resonance imaging (fMRI) at sub-millimeter resolution while maintaining high spatial coverage and acceptable signal-to-noise ratio. Here, we examine whether ultra-high-resolution fMRI can be exploited for routine use in neuroscience research. We conducted fMRI in human visual cortex during a simple event-related visual experiment (7T, gradient-echo EPI, 0.8-mm isotropic voxels, 2.2-s sampling rate, 84 slices), and developed analysis and visualization tools to assess the quality of the data. We make three main observations. First, we find that the acquired fMRI images, combined with appropriate surface-based processing, provide reliable and accurate measurements of fine-scale blood oxygenation level dependent (BOLD) activity patterns. Second, we show that the highly folded structure of cortex causes substantial biases on spatial resolution and data visualization. Third, we examine the well-recognized issue of venous contributions to fMRI signals. In a systematic assessment of large sections of cortex measured at a fine scale, we show that time-averaged T2*-weighted EPI intensity is a simple, robust marker of venous effects. These venous effects are unevenly distributed across cortex, are more pronounced in gyri and outer cortical depths, and are, to a certain degree, in consistent locations across subjects relative to cortical folding. Furthermore, we show that these venous effects are strongly correlated with BOLD responses evoked by the experiment. We conclude that ultra-high-resolution fMRI can provide robust information about fine-scale BOLD activity patterns, but special care must be exercised in visualizing and interpreting these patterns, especially with regards to the confounding influence of the brain’s vasculature. To help translate these methodological findings to neuroscience research, we provide practical suggestions for both high-resolution and standard-resolution fMRI studies.

scholarly journals TDM: a temporal decomposition method for removing venous effects from task-based fMRI

2019 ◽  
Author(s):  
Kendrick Kay ◽  
Keith W. Jamison ◽  
Ruyuan Zhang ◽  
Kamil Ugurbil
Keyword(s):  
High Resolution ◽  
Spin Echo ◽  
Pulse Sequences ◽  
High Sensitivity ◽  
Blood Oxygenation ◽  
Dimensional Manifold ◽  
Spatial Accuracy ◽  
Gradient Echo ◽  
Spatial Coverage ◽  
Temporal Decomposition

AbstractMost functional magnetic resonance imaging (fMRI) is conducted with gradient-echo pulse sequences. Although this yields high sensitivity to blood oxygenation level dependent (BOLD) signals, gradient-echo acquisitions are heavily influenced by venous effects which limit the ultimate spatial resolution and spatial accuracy of fMRI. While alternative acquisition methods such as spin-echo can be used to mitigate venous effects, these methods lead to serious reductions in signal-to-noise ratio and spatial coverage, and are difficult to implement without leakage of undesirable non-spin-echo effects into the data. Moreover, analysis heuristics such as masking veins or sampling inner cortical depths using high-resolution fMRI may be helpful, but sacrifice information from many parts of the brain. Here, we describe a new analysis method that is compatible with conventional gradient-echo acquisition and provides venous-free response estimates throughout the entire imaged volume. The method involves fitting a low-dimensional manifold characterizing variation in response timecourses observed in a given dataset, and then using identified early and late timecourses as basis functions for decomposing responses into components related to the microvasculature (capillaries and small venules) and the macrovasculature (veins), respectively. We show that this Temporal Decomposition through Manifold Fitting (TDM) method is robust, consistently deriving meaningful timecourses in individual fMRI scan sessions. Moreover, we show that by removing late components, TDM substantially reduces the superficial cortical depth bias present in gradient-echo BOLD responses and eliminates artifacts in cortical activity maps. TDM is general: it can be applied to any task-based fMRI experiment, can be used with standard- or high-resolution fMRI acquisitions, and can even be used to remove residual venous effects from specialized acquisition methods like spin-echo. We suggest that TDM is a powerful method that improves the spatial accuracy of fMRI and provides insight into the origins of the BOLD signal.

scholarly journals A snapping shrimp has the fastest vision of any aquatic animal

2020 ◽  
Vol 16 (6) ◽  
pp. 20200298
Author(s):  
Alexandra C. N. Kingston ◽  
Daniel R. Chappell ◽  
Daniel I. Speiser
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Activity Patterns ◽  
Sampling Rate ◽  
Light Level ◽  
Sensory Systems ◽  
Aquatic Animal ◽  
Snapping Shrimp ◽  
Temporal Sampling ◽  
Broad Dynamic Range

Animals use their sensory systems to sample information from their environments. The physiological properties of sensory systems differ, leading animals to perceive their environments in different ways. For example, eyes have different temporal sampling rates, with faster-sampling eyes able to resolve faster-moving scenes. Eyes can also have different dynamic ranges. For every eye, there is a light level below which vision is unreliable because of an insufficient signal-to-noise ratio and a light level above which the photoreceptors are saturated. Here, we report that the eyes of the snapping shrimp Alpheus heterochaelis have a temporal sampling rate of at least 160 Hz, making them the fastest-sampling eyes ever described in an aquatic animal. Fast-sampling eyes help flying animals detect objects moving across their retinas at high angular velocities. A. heterochaelis are fast-moving animals that live in turbid, structurally complex oyster reefs and their fast-sampling eyes, like those of flying animals, may help them detect objects moving rapidly across their retinas. We also report that the eyes of A. heterochaelis have a broad dynamic range that spans conditions from late twilight (approx. 1 lux) to direct sunlight (approx. 100 000 lux), a finding consistent with the circatidal activity patterns of this shallow-dwelling species.

scholarly journals Lidar reveals activity anomaly of malaria vectors during pan-African eclipse

2020 ◽  
Vol 6 (20) ◽  
pp. eaay5487 ◽  
Author(s):  
Mikkel Brydegaard ◽  
Samuel Jansson ◽  
Elin Malmqvist ◽  
Yeromin P. Mlacha ◽  
Alem Gebru ◽  
...  
Keyword(s):  
High Resolution ◽  
Activity Patterns ◽  
Malaria Vectors ◽  
Fine Scale ◽  
Vector Ecology ◽  
Pan African ◽  
Insect Activity ◽  
Annular Solar Eclipse

Yearly, a quarter billion people are infected and a half a million killed by the mosquito-borne disease malaria. Lack of real-time observational tools for continuously assessing the unperturbed mosquito flight activity in situ limits progress toward improved vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect adjacent to a Tanzanian village. We evaluated one-third million insect observations during five nights, four days, and one annular solar eclipse. We demonstrate in situ lidar classification of several insect families and their sexes based on their modulation signatures. We were able to compare the fine-scale spatiotemporal activity patterns of malaria vectors during ordinary days and an eclipse to disentangle phototactic activity patterns from the circadian mechanism. We observed an increased insect activity during the eclipse attributable to mosquitoes. These unprecedented findings demonstrate how lidar-based monitoring of distinct mosquito activities could advance our understanding of vector ecology.

High Resolution Stereography of Complementary Freeze-Fracture Replicas Reveals the Presence of Depressions Opposite Membrane Associated Particles of Split Membranes

1971 ◽  
Vol 29 ◽  
pp. 442-443
Author(s):  
Russell L. Steere
Keyword(s):  
High Resolution ◽  
Cardiac Muscle ◽  
Electron Micrographs ◽  
Chromic Acid ◽  
Freeze Fracture ◽  
Distilled Water ◽  
Fine Scale ◽  
Acid Cleaning ◽  
Cleaning Solution

Complementary replicas have revealed the fact that the two common faces observed in electron micrographs of freeze-fracture and freeze-etch specimens are complementary to each other and are thus the new faces of a split membrane rather than the original inner and outer surfaces (1, 2 and personal observations). The big question raised by published electron micrographs is why do we not see depressions in the complementary face opposite membrane-associated particles? Reports have appeared indicating that some depressions do appear but complementarity on such a fine scale has yet to be shown.Dog cardiac muscle was perfused with glutaraldehyde, washed in distilled water, then transferred to 30% glycerol (material furnished by Dr. Joaquim Sommer, Duke Univ., and VA Hospital, Durham, N.C.). Small strips were freeze-fractured in a Denton Vacuum DFE-2 Freeze-Etch Unit with complementary replica tooling. Replicas were cleaned in chromic acid cleaning solution, then washed in 4 changes of distilled water and mounted on opposite sides of the center wire of a Formvar-coated grid.

Progress in high-resolution CRYO-SEM imaging of viral particles

1996 ◽  
Vol 54 ◽  
pp. 818-819
Author(s):  
Ya Chen ◽  
Geoffrey Letchworth ◽  
John White
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
Structural Information ◽  
Signal To Noise Ratio ◽  
Flexible Structures ◽  
Simian Virus ◽  
Topographic Features ◽  
Viral Particles ◽  
Scanning Electron

Low-temperature high-resolution scanning electron microscopy (cryo-HRSEM) has been successfully utilized to image biological macromolecular complexes at nanometer resolution. Recently, imaging of individual viral particles such as reovirus using cryo-HRSEM or simian virus (SIV) using HRSEM, HV-STEM and AFM have been reported. Although conventional electron microscopy (e.g., negative staining, replica, embedding and section), or cryo-TEM technique are widely used in studying of the architectures of viral particles, scanning electron microscopy presents two major advantages. First, secondary electron signal of SEM represents mostly surface topographic features. The topographic details of a biological assembly can be viewed directly and will not be obscured by signals from the opposite surface or from internal structures. Second, SEM may produce high contrast and signal-to-noise ratio images. As a result of this important feature, it is capable of visualizing not only individual virus particles, but also asymmetric or flexible structures. The 2-3 nm resolution obtained using high resolution cryo-SEM made it possible to provide useful surface structural information of macromolecule complexes within cells and tissues. In this study, cryo-HRSEM is utilized to visualize the distribution of glycoproteins of a herpesvirus.

scholarly journals Ultrastructural visualization of cytoskeletal mRNAs and their associated proteins using double-label in situ hybridization.

1989 ◽  
Vol 108 (6) ◽  
pp. 2343-2353 ◽  
Author(s):  
R H Singer ◽  
G L Langevin ◽  
J B Lawrence
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Colloidal Gold ◽  
Messenger Rna ◽  
Signal To Noise Ratio ◽  
Simultaneous Detection ◽  
Gold Particles ◽  
Rna Molecules ◽  
Nucleic Acid Molecule

We have been able to visualize cytoskeletal messenger RNA molecules at high resolution using nonisotopic in situ hybridization followed by whole-mount electron microscopy. Biotinated cDNA probes for actin, tubulin, or vimentin mRNAs were hybridized to Triton-extracted chicken embryo fibroblasts and myoblasts. The cells were then exposed to antibodies against biotin followed by colloidal gold-conjugated antibodies and then critical-point dried. Identification of mRNA was possible using a probe fragmented to small sizes such that hybridization of several probe fragments along the mRNA was detected as a string of colloidal gold particles qualitatively and quantitatively distinguishable from nonspecific background. Extensive analysis showed that when eight gold particles were seen in this iterated array, the signal to noise ratio was greater than 30:1. Furthermore, these gold particles were colinear, often spiral, or circular suggesting detection of a single nucleic acid molecule. Antibodies against actin, vimentin, or tubulin proteins were used after in situ hybridization, allowing simultaneous detection of the protein and its cognate message on the same sample. This revealed that cytoskeletal mRNAs are likely to be extremely close to actin protein (5 nm or less) and unlikely to be within 20 nm of vimentin or tubulin filaments. Actin mRNA was found to be more predominant in lamellipodia of motile cells, confirming previous results. These results indicate that this high resolution in situ hybridization approach is a powerful tool by which to investigate the association of mRNA with the cytoskeleton.

Very high resolution environmental predictors in species distribution models

2013 ◽  
Vol 38 (1) ◽  
pp. 79-96 ◽  
Author(s):  
Jean-Nicolas Pradervand ◽  
Anne Dubuis ◽  
Loïc Pellissier ◽  
Antoine Guisan ◽  
Christophe Randin
Keyword(s):  
High Resolution ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Environmental Data ◽  
Swiss Alps ◽  
Fine Scale ◽  
Distribution Models ◽  
Model Quality ◽  
Vegetation Height ◽  
Very High

Recent advances in remote sensing technologies have facilitated the generation of very high resolution (VHR) environmental data. Exploratory studies suggested that, if used in species distribution models (SDMs), these data should enable modelling species’ micro-habitats and allow improving predictions for fine-scale biodiversity management. In the present study, we tested the influence, in SDMs, of predictors derived from a VHR digital elevation model (DEM) by comparing the predictive power of models for 239 plant species and their assemblages fitted at six different resolutions in the Swiss Alps. We also tested whether changes of the model quality for a species is related to its functional and ecological characteristics. Refining the resolution only contributed to slight improvement of the models for more than half of the examined species, with the best results obtained at 5 m, but no significant improvement was observed, on average, across all species. Contrary to our expectations, we could not consistently correlate the changes in model performance with species characteristics such as vegetation height. Temperature, the most important variable in the SDMs across the different resolutions, did not contribute any substantial improvement. Our results suggest that improving resolution of topographic data only is not sufficient to improve SDM predictions – and therefore local management – compared to previously used resolutions (here 25 and 100 m). More effort should be dedicated now to conduct finer-scale in-situ environmental measurements (e.g. for temperature, moisture, snow) to obtain improved environmental measurements for fine-scale species mapping and management.

scholarly journals Information Entropy- and Average-Based High-Resolution Digital Storage Oscilloscope

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Jun Jiang ◽  
Lianping Guo ◽  
Kuojun Yang ◽  
Huiqing Pan
Keyword(s):  
Data Fusion ◽  
Information Entropy ◽  
Signal To Noise Ratio ◽  
Sampling Rate ◽  
Storage Oscilloscope ◽  
Whole Process ◽  
Digital Storage ◽  
Gross Error ◽  
Digital Storage Oscilloscope ◽  
Sample Data

Vertical resolution is an essential indicator of digital storage oscilloscope (DSO) and the key to improving resolution is to increase digitalizing bits and lower noise. Averaging is a typical method to improve signal to noise ratio (SNR) and the effective number of bits (ENOB). The existing averaging algorithm is apt to be restricted by the repetitiveness of signal and be influenced by gross error in quantization, and therefore its effect on restricting noise and improving resolution is limited. An information entropy-based data fusion and average-based decimation filtering algorithm, proceeding from improving average algorithm and in combination with relevant theories of information entropy, are proposed in this paper to improve the resolution of oscilloscope. For single acquiring signal, resolution is improved through eliminating gross error in quantization by utilizing the maximum entropy of sample data with further noise filtering via average-based decimation after data fusion of efficient sample data under the premise of oversampling. No subjective assumptions and constraints are added to the signal under test in the whole process without any impact on the analog bandwidth of oscilloscope under actual sampling rate.

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