Toward an MRI-Based Mesoscale Connectome of the Squid Brain.
Ontology highlight
ABSTRACT:
SUBMITTER: Chung WS
PROVIDER: S-EPMC6974791 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease.
| S-EPMC5102064 | biostudies-literature
Project description:Traumatic brain injury (TBI) is often characterized by alterations in brain connectivity. We explored connectivity alterations from a network perspective, using graph theory, and examined whether injury severity affected structural connectivity and modulated the association between brain connectivity and cognitive deficits post-TBI. We performed diffusion imaging network analysis on chronic TBI patients, with different injury severities and healthy subjects. From both global and local perspectives, we found an effect of injury severity on network strength. In addition, regions which were considered as hubs differed between groups. Further exploration of graph measures in the determined hub regions showed that efficiency of six regions differed between groups. An association between reduced efficiency in the precuneus and nonverbal abstract reasoning deficits (calculated using actual pre-injury scores) was found in the controls but was lost in TBI patients. Our results suggest that disconnection of network hubs led to a less efficient network, which in turn may have contributed to the cognitive impairments manifested in TBI patients. We conclude that injury severity modulates the disruption of network organization, reflecting a "dose response" relationship and emphasize the role of efficiency as an important diagnostic tool to detect subtle brain injury specifically in mild TBI patients.
| S-EPMC7272462 | biostudies-literature
Project description:Ultra-high field magnetic resonance imaging (MRI) became increasingly relevant for in vivo neuroscientific research because of improved spatial resolutions. However, this is still the unchallenged domain of histological studies, which long played an important role in the investigation of neuropsychiatric disorders. While the field of biological psychiatry strongly advanced on macroscopic levels, current developments are rediscovering the richness of immunohistological information when attempting a multi-level systematic approach to brain function and dysfunction. For most studies, histology sections lost information on three-dimensional reconstructions. Translating histological sections to 3D-volumes would thus not only allow for multi-stain and multi-subject alignment in post mortem data, but also provide a crucial step in big data initiatives involving the network analyses currently performed with in vivo MRI. We therefore investigated potential pitfalls during integration of MR and histological information where no additional blockface information is available. We demonstrated that strengths and requirements from both methods can be effectively combined at a spatial resolution of 200 μm. However, the success of this approach is heavily dependent on choices of hardware, sequence and reconstruction. We provide a fully automated pipeline that optimizes histological 3D reconstructions, providing a potentially powerful solution not only for primary human post mortem research institutions in neuropsychiatric research, but also to help alleviate the massive workloads in neuroanatomical atlas initiatives. We further demonstrate (for the first time) the feasibility and quality of ultra-high spatial resolution (150 μm isotopic) imaging of the entire human brain MRI at 7T, offering new opportunities for analyses on MR-derived information.
| S-EPMC3784919 | biostudies-literature
Project description:Diffusion MRI has evolved towards an important clinical diagnostic and research tool. Though clinical routine is using mainly diffusion weighted and tensor imaging approaches, Q-ball imaging and diffusion spectrum imaging techniques have become more widely available. They are frequently used in research-oriented investigations in particular those aiming at measuring brain network connectivity. In this work, we aim at assessing the dependency of connectivity measurements on various diffusion encoding schemes in combination with appropriate data modeling. We process and compare the structural connection matrices computed from several diffusion encoding schemes, including diffusion tensor imaging, q-ball imaging and high angular resolution schemes, such as diffusion spectrum imaging with a publically available processing pipeline for data reconstruction, tracking and visualization of diffusion MR imaging. The results indicate that the high angular resolution schemes maximize the number of obtained connections when applying identical processing strategies to the different diffusion schemes. Compared to the conventional diffusion tensor imaging, the added connectivity is mainly found for pathways in the 50-100mm range, corresponding to neighboring association fibers and long-range associative, striatal and commissural fiber pathways. The analysis of the major associative fiber tracts of the brain reveals striking differences between the applied diffusion schemes. More complex data modeling techniques (beyond tensor model) are recommended 1) if the tracts of interest run through large fiber crossings such as the centrum semi-ovale, or 2) if non-dominant fiber populations, e.g. the neighboring association fibers are the subject of investigation. An important finding of the study is that since the ground truth sensitivity and specificity is not known, the comparability between results arising from different strategies in data reconstruction and/or tracking becomes implausible to understand.
| S-EPMC3779224 | biostudies-literature
Project description:ObjectiveTo investigate structural and functional neural organization in amyotrophic lateral sclerosis (ALS), primary lateral sclerosis (PLS), and progressive muscular atrophy (PMA).MethodsA total of 173 patients with sporadic ALS, 38 patients with PLS, 28 patients with PMA, and 79 healthy controls were recruited from 3 Italian centers. Participants underwent clinical, neuropsychological, and brain MRI evaluations. Using graph analysis and connectomics, global and lobar topologic network properties and regional structural and functional brain connectivity were assessed. The association between structural and functional network organization and clinical and cognitive data was investigated.ResultsCompared with healthy controls, patients with ALS and patients with PLS showed altered structural global network properties, as well as local topologic alterations and decreased structural connectivity in sensorimotor, basal ganglia, frontal, and parietal areas. Patients with PMA showed preserved global structure. Patient groups did not show significant alterations of functional network topologic properties relative to controls. Increased local functional connectivity was observed in patients with ALS in the precentral, middle, and superior frontal areas, and in patients with PLS in the sensorimotor, basal ganglia, and temporal networks. In patients with ALS and patients with PLS, structural connectivity alterations correlated with motor impairment, whereas functional connectivity disruption was closely related to executive dysfunction and behavioral disturbances.ConclusionsThis multicenter study showed widespread motor and extramotor network degeneration in ALS and PLS, suggesting that graph analysis and connectomics might represent a powerful approach to detect upper motor neuron degeneration, extramotor brain changes, and network reorganization associated with the disease. Network-based advanced MRI provides an objective in vivo assessment of motor neuron diseases, delivering potential prognostic markers.
| S-EPMC7682834 | biostudies-literature
Project description:Interest in structural brain connectivity has grown with the understanding that abnormal neural connections may play a role in neurologic and psychiatric diseases. Small animal connectivity mapping techniques are particularly important for identifying aberrant connectivity in disease models. Diffusion magnetic resonance imaging tractography can provide nondestructive, 3D, brain-wide connectivity maps, but has historically been limited by low spatial resolution, low signal-to-noise ratio, and the difficulty in estimating multiple fiber orientations within a single image voxel. Small animal diffusion tractography can be substantially improved through the combination of ex vivo MRI with exogenous contrast agents, advanced diffusion acquisition and reconstruction techniques, and probabilistic fiber tracking. Here, we present a comprehensive, probabilistic tractography connectome of the mouse brain at microscopic resolution, and a comparison of these data with a neuronal tracer-based connectivity data from the Allen Brain Atlas. This work serves as a reference database for future tractography studies in the mouse brain, and demonstrates the fundamental differences between tractography and neuronal tracer data.
| S-EPMC4715247 | biostudies-literature
Project description:We have developed a way to map brain-wide networks using focal pulsed infrared neural stimulation in ultrahigh-field magnetic resonance imaging (MRI). The patterns of connections revealed are similar to those of connections previously mapped with anatomical tract tracing methods. These include connections between cortex and subcortical locations and long-range cortico-cortical connections. Studies of local cortical connections reveal columnar-sized laminar activation, consistent with feed-forward and feedback projection signatures. This method is broadly applicable and can be applied to multiple areas of the brain in different species and across different MRI platforms. Systematic point-by-point application of this method may lead to fundamental advances in our understanding of brain connectomes.
| S-EPMC6482007 | biostudies-literature
Project description:Diffusion MRI (dMRI)-based tractography offers unique abilities to map whole-brain structural connections in human and animal brains. However, dMRI-based tractography indirectly measures white matter tracts, with suboptimal accuracy and reliability. Recently, sophisticated methods including constrained spherical deconvolution (CSD) and global tractography have been developed to improve tract reconstructions through modeling of more complex fiber orientations. Our study aimed to determine the accuracy of connectome reconstruction for three dMRI-based tractography approaches: diffusion tensor (DT)-based, CSD-based and global tractography. Therefore, we validated whole brain structural connectome reconstructions based on ten ultrahigh-resolution dMRI rat brain scans and 106 cortical regions, from which varying tractography parameters were compared against standardized neuronal tracer data. All tested tractography methods generated considerable numbers of false positive and false negative connections. There was a parameter range trade-off between sensitivity: 0.06-0.63 interhemispherically and 0.22-0.86 intrahemispherically; and specificity: 0.99-0.60 interhemispherically and 0.99-0.23 intrahemispherically. Furthermore, performance of all tractography methods decreased with increasing spatial distance between connected regions. Similar patterns and trade-offs were found, when we applied spherical deconvolution informed filtering of tractograms, streamline thresholding and group-based average network thresholding. Despite the potential of CSD-based and global tractography to handle complex fiber orientations at voxel level, reconstruction accuracy, especially for long-distance connections, remains a challenge. Hence, connectome reconstruction benefits from varying parameter settings and combination of tractography methods to account for anatomical variation of neuronal pathways.
| S-EPMC5968063 | biostudies-literature
Project description:We provide a comprehensive diffusion MRI dataset acquired with a novel biomimetic phantom mimicking human white matter. The fiber substrates in the diffusion phantom were constructed from hollow textile axons ("taxons") with an inner diameter of 11.8±1.2?µm and outer diameter of 33.5±2.3?µm. Data were acquired on the 3?T CONNECTOM MRI scanner with multiple diffusion times and multiple q-values per diffusion time, which is a dedicated acquisition for validation of microstructural imaging methods, such as compartment size and volume fraction mapping. Minimal preprocessing was performed to correct for susceptibility and eddy current distortions. Data were deposited in the XNAT Central database (project ID: dMRI_Phant_MGH).
| S-EPMC5996223 | biostudies-literature
Project description:The question of whether there are biological differences between male and female brains is a fraught one, and political positions and prior expectations seem to have a strong influence on the interpretation of scientific data in this field. This question is relevant to issues of gender differences in the prevalence of psychiatric conditions, including autism, attention deficit hyperactivity disorder (ADHD), Tourette's syndrome, schizophrenia, dyslexia, depression, and eating disorders. Understanding how gender influences vulnerability to these conditions is significant. Diffusion magnetic resonance imaging (dMRI) provides a non-invasive method to investigate brain microstructure and the integrity of anatomical connectivity. Generalized q-sampling imaging (GQI) has been proposed to characterize complicated fiber patterns and distinguish fiber orientations, providing an opportunity for more accurate, higher-order descriptions through the water diffusion process. Therefore, we aimed to investigate differences in the brain's structural network between teenage males and females using GQI. This study included 59 (i.e., 33 males and 26 females) age- and education-matched subjects (age range: 13 to 14 years). The structural connectome was obtained by graph theoretical and network-based statistical (NBS) analyses. Our findings show that teenage male brains exhibit better intrahemispheric communication, and teenage female brains exhibit better interhemispheric communication. Our results also suggest that the network organization of teenage male brains is more local, more segregated, and more similar to small-world networks than teenage female brains. We conclude that the use of an MRI study with a GQI-based structural connectomic approach like ours presents novel insights into network-based systems of the brain and provides a new piece of the puzzle regarding gender differences.
| S-EPMC5447512 | biostudies-literature