scholarly journals Journey into the brain: from single synapse to whole brain anatomy by correlative microscopy

2014 ◽  
Author(s):  
Francesco Pavone
Keyword(s):  
Brain Anatomy ◽  
Correlative Microscopy ◽  
Whole Brain ◽  
The Brain ◽  
Single Synapse

scholarly journals Content-Based Estimation of Brain MRI Tilt in Three Orthogonal Directions

2021 ◽  
Author(s):  
Pooja Prabhu ◽  
A. K. Karunakar ◽  
Sanjib Sinha ◽  
N. Mariyappa ◽  
G. K. Bhargava ◽  
...  
Keyword(s):  
Large Scale ◽  
Brain Mri ◽  
Similarity Measures ◽  
Principal Component ◽  
Brain Anatomy ◽  
Morphological Operations ◽  
Mr Images ◽  
Tilt Correction ◽  
Brain Mr Images ◽  
The Brain

AbstractIn a general scenario, the brain images acquired from magnetic resonance imaging (MRI) may experience tilt, distorting brain MR images. The tilt experienced by the brain MR images may result in misalignment during image registration for medical applications. Manually correcting (or estimating) the tilt on a large scale is time-consuming, expensive, and needs brain anatomy expertise. Thus, there is a need for an automatic way of performing tilt correction in three orthogonal directions (X, Y, Z). The proposed work aims to correct the tilt automatically by measuring the pitch angle, yaw angle, and roll angle in X-axis, Z-axis, and Y-axis, respectively. For correction of the tilt around the Z-axis (pointing to the superior direction), image processing techniques, principal component analysis, and similarity measures are used. Also, for correction of the tilt around the X-axis (pointing to the right direction), morphological operations, and tilt correction around the Y-axis (pointing to the anterior direction), orthogonal regression is used. The proposed approach was applied to adjust the tilt observed in the T1- and T2-weighted MR images. The simulation study with the proposed algorithm yielded an error of 0.40 ± 0.09°, and it outperformed the other existing studies. The tilt angle (in degrees) obtained is ranged from 6.2 ± 3.94, 2.35 ± 2.61, and 5 ± 4.36 in X-, Z-, and Y-directions, respectively, by using the proposed algorithm. The proposed work corrects the tilt more accurately and robustly when compared with existing studies.

scholarly journals Alzheimer’s Disease Projection From Normal to Mild Dementia Reflected in Functional Network Connectivity: A Longitudinal Study

2021 ◽  
Vol 14 ◽  
Author(s):  
Mohammad S. E. Sendi ◽  
Elaheh Zendehrouh ◽  
Robyn L. Miller ◽  
Zening Fu ◽  
Yuhui Du ◽  
...  
Keyword(s):  
Default Mode Network ◽  
Early Stage ◽  
Network Connectivity ◽  
Functional Network ◽  
Normal Brain ◽  
Whole Brain ◽  
Mild Dementia ◽  
Sensorimotor Network ◽  
Functional Network Connectivity ◽  
The Brain

BackgroundAlzheimer’s disease (AD) is the most common age-related problem and progresses in different stages, including mild cognitive impairment (early stage), mild dementia (middle-stage), and severe dementia (late-stage). Recent studies showed changes in functional network connectivity obtained from resting-state functional magnetic resonance imaging (rs-fMRI) during the transition from healthy aging to AD. By assuming that the brain interaction is static during the scanning time, most prior studies are focused on static functional or functional network connectivity (sFNC). Dynamic functional network connectivity (dFNC) explores temporal patterns of functional connectivity and provides additional information to its static counterpart.MethodWe used longitudinal rs-fMRI from 1385 scans (from 910 subjects) at different stages of AD (from normal to very mild AD or vmAD). We used group-independent component analysis (group-ICA) and extracted 53 maximally independent components (ICs) for the whole brain. Next, we used a sliding-window approach to estimate dFNC from the extracted 53 ICs, then group them into 3 different brain states using a clustering method. Then, we estimated a hidden Markov model (HMM) and the occupancy rate (OCR) for each subject. Finally, we investigated the link between the clinical rate of each subject with state-specific FNC, OCR, and HMM.ResultsAll states showed significant disruption during progression normal brain to vmAD one. Specifically, we found that subcortical network, auditory network, visual network, sensorimotor network, and cerebellar network connectivity decrease in vmAD compared with those of a healthy brain. We also found reorganized patterns (i.e., both increases and decreases) in the cognitive control network and default mode network connectivity by progression from normal to mild dementia. Similarly, we found a reorganized pattern of between-network connectivity when the brain transits from normal to mild dementia. However, the connectivity between visual and sensorimotor network connectivity decreases in vmAD compared with that of a healthy brain. Finally, we found a normal brain spends more time in a state with higher connectivity between visual and sensorimotor networks.ConclusionOur results showed the temporal and spatial pattern of whole-brain FNC differentiates AD form healthy control and suggested substantial disruptions across multiple dynamic states. In more detail, our results suggested that the sensory network is affected more than other brain network, and default mode network is one of the last brain networks get affected by AD In addition, abnormal patterns of whole-brain dFNC were identified in the early stage of AD, and some abnormalities were correlated with the clinical score.

scholarly journals Scatterometry Measurements With Scattered Light Imaging Enable New Insights Into the Nerve Fiber Architecture of the Brain

2021 ◽  
Vol 15 ◽  
Author(s):  
Miriam Menzel ◽  
Marouan Ritzkowski ◽  
Jan A. Reuter ◽  
David Gräßel ◽  
Katrin Amunts ◽  
...  
Keyword(s):  
Human Brain ◽  
Nerve Fiber ◽  
Brain Tissue ◽  
Scattered Light ◽  
Polar Angle ◽  
Nerve Fibers ◽  
Fiber Architecture ◽  
Whole Brain ◽  
Tissue Samples ◽  
The Brain

The correct reconstruction of individual (crossing) nerve fibers is a prerequisite when constructing a detailed network model of the brain. The recently developed technique Scattered Light Imaging (SLI) allows the reconstruction of crossing nerve fiber pathways in whole brain tissue samples with micrometer resolution: the individual fiber orientations are determined by illuminating unstained histological brain sections from different directions, measuring the transmitted scattered light under normal incidence, and studying the light intensity profiles of each pixel in the resulting image series. So far, SLI measurements were performed with a fixed polar angle of illumination and a small number of illumination directions, providing only an estimate of the nerve fiber directions and limited information about the underlying tissue structure. Here, we use a display with individually controllable light-emitting diodes to measure the full distribution of scattered light behind the sample (scattering pattern) for each image pixel at once, enabling scatterometry measurements of whole brain tissue samples. We compare our results to coherent Fourier scatterometry (raster-scanning the sample with a non-focused laser beam) and previous SLI measurements with fixed polar angle of illumination, using sections from a vervet monkey brain and human optic tracts. Finally, we present SLI scatterometry measurements of a human brain section with 3 μm in-plane resolution, demonstrating that the technique is a powerful approach to gain new insights into the nerve fiber architecture of the human brain.

scholarly journals Increased sensitivity to strong perturbations in a whole-brain model of LSD

2021 ◽  
Author(s):  
Beatrice M. Jobst ◽  
Selen Atasoy ◽  
Adrián Ponce-Alvarez ◽  
Ana Sanjuán ◽  
Leor Roseman ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
External Perturbation ◽  
Brain Regions ◽  
Lysergic Acid ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Whole Brain ◽  
Response Diversity ◽  
Brain States ◽  
The Brain

AbstractLysergic acid diethylamide (LSD) is a potent psychedelic drug, which has seen a revival in clinical and pharmacological research within recent years. Human neuroimaging studies have shown fundamental changes in brain-wide functional connectivity and an expansion of dynamical brain states, thus raising the question about a mechanistic explanation of the dynamics underlying these alterations. Here, we applied a novel perturbational approach based on a whole-brain computational model, which opens up the possibility to externally perturb different brain regions in silico and investigate differences in dynamical stability of different brain states, i.e. the dynamical response of a certain brain region to an external perturbation. After adjusting the whole-brain model parameters to reflect the dynamics of functional magnetic resonance imaging (fMRI) BOLD signals recorded under the influence of LSD or placebo, perturbations of different brain areas were simulated by either promoting or disrupting synchronization in the regarding brain region. After perturbation offset, we quantified the recovery characteristics of the brain area to its basal dynamical state with the Perturbational Integration Latency Index (PILI) and used this measure to distinguish between the two brain states. We found significant changes in dynamical complexity with consistently higher PILI values after LSD intake on a global level, which indicates a shift of the brain’s global working point further away from a stable equilibrium as compared to normal conditions. On a local level, we found that the largest differences were measured within the limbic network, the visual network and the default mode network. Additionally, we found a higher variability of PILI values across different brain regions after LSD intake, indicating higher response diversity under LSD after an external perturbation. Our results provide important new insights into the brain-wide dynamical changes underlying the psychedelic state - here provoked by LSD intake - and underline possible future clinical applications of psychedelic drugs in particular psychiatric disorders.HighlightsNovel offline perturbational method applied on functional magnetic resonance imaging (fMRI) data under the effect of lysergic acid diethylamide (LSD)Shift of brain’s global working point to more complex dynamics after LSD intakeConsistently longer recovery time after model perturbation under LSD influenceStrongest effects in resting state networks relevant for psychedelic experienceHigher response diversity across brain regions under LSD influence after an external in silico perturbation

scholarly journals Leveling up: improving power in fMRI by moving beyond cluster-level inference

2021 ◽  
Author(s):  
Stephanie Noble ◽  
Mandy Mejia ◽  
Andrew Zalesky ◽  
Dustin Scheinost
Keyword(s):  
Average Effect ◽  
Brain Areas ◽  
Whole Brain ◽  
Typical Sample ◽  
Human Connectome Project ◽  
Inference Network ◽  
The Brain ◽  
Cluster Level ◽  
Human Neuroimaging ◽  
Adequate Power

Inference in neuroimaging commonly occurs at the level of "clusters" of neighboring voxels or connections, thought to reflect functionally specific brain areas. Yet increasingly large studies reveal effects that are shared throughout the brain, suggesting that reported clusters may only reflect the "tip of the iceberg" of underlying effects. Here, we empirically compare power of traditional levels of inference (edge and cluster) with broader levels of inference (network and whole-brain) by resampling functional connectivity data from the Human Connectome Project (n=40, 80, 120). Only network- and whole brain-level inference attained or surpassed "adequate" power (β =80%) to detect an average effect, with almost double the power for network- compared with cluster-level procedures at more typical sample sizes. Likewise, effects tended to be widespread, and more widespread pooling resulted in stronger magnitude effects. Power also substantially increased when controlling FDR rather than FWER. Importantly, there may be similar implications for task-based activation analyses where effects are also increasingly understood to be widespread. However, increased power with broader levels of inference may diminish the specificity to localize effects, especially for non-task contexts. These findings underscore the benefit of shifting the scale of inference to better capture the underlying signal, which may unlock opportunities for discovery in human neuroimaging.

scholarly journals Exploring the dynamic mechanisms of steady-state visual evoked potentials at the whole-brain level: evidence from a computational study

2021 ◽  
Author(s):  
Ge Zhang ◽  
Yan Cui ◽  
Yangsong Zhang ◽  
Hefei Cao ◽  
Guanyu Zhou ◽  
...  
Keyword(s):  
Steady State ◽  
Evoked Potentials ◽  
Visual Evoked Potentials ◽  
Large Scale ◽  
Whole Brain ◽  
Frequency Sensitivity ◽  
Dynamic Mechanisms ◽  
Brain Level ◽  
The Brain ◽  
Visual Evoked

AbstractPeriodic visual stimulation can induce stable steady-state visual evoked potentials (SSVEPs) distributed in multiple brain regions and has potential applications in both neural engineering and cognitive neuroscience. However, the underlying dynamic mechanisms of SSVEPs at the whole-brain level are still not completely understood. Here, we addressed this issue by simulating the rich dynamics of SSVEPs with a large-scale brain model designed with constraints of neuroimaging data acquired from the human brain. By eliciting activity of the occipital areas using an external periodic stimulus, our model was capable of replicating both the spatial distributions and response features of SSVEPs that were observed in experiments. In particular, we confirmed that alpha-band (8-12 Hz) stimulation could evoke stronger SSVEP responses; this frequency sensitivity was due to nonlinear resonance and could be modulated by endogenous factors in the brain. Interestingly, the stimulus-evoked brain networks also exhibited significant superiority in topological properties near this frequency-sensitivity range, and stronger SSVEP responses were demonstrated to be supported by more efficient functional connectivity at the neural activity level. These findings not only provide insights into the mechanistic understanding of SSVEPs at the whole-brain level but also indicate a bright future for large-scale brain modeling in characterizing the complicated dynamics and functions of the brain.

scholarly journals Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling

2015 ◽  
Vol 11 (8) ◽  
pp. e1004445 ◽  
Author(s):  
Adrián Ponce-Alvarez ◽  
Biyu J. He ◽  
Patric Hagmann ◽  
Gustavo Deco
Keyword(s):  
Cortical Activity ◽  
Activity Space ◽  
Whole Brain ◽  
Brain Modeling ◽  
The Brain

Contributions of Developmental Studies in the DogfishScyliorhinus caniculato the Brain Anatomy of Elasmobranchs: Insights on the Basal Ganglia

2012 ◽  
Vol 80 (2) ◽  
pp. 127-141 ◽  
Author(s):  
Idoia Quintana-Urzainqui ◽  
Catalina Sueiro ◽  
Ivan Carrera ◽  
Susana Ferreiro-Galve ◽  
Gabriel Santos-Durán ◽  
...  
Keyword(s):  
Basal Ganglia ◽  
Brain Anatomy ◽  
Developmental Studies ◽  
The Brain
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