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Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda.

ABSTRACT: Simulation of large-scale networks of neurons is an important approach to understanding and interpreting experimental data from healthy and diseased brains. Owing to the rapid development of simulation software and the accumulation of quantitative data of different neuronal types, it is possible to predict both computational and dynamical properties of local microcircuits in a 'bottom-up' manner. Simulated data from these models can be compared with experiments and 'top-down' modelling approaches, successively bridging the scales. Here we describe an open source pipeline, using the software Snudda, for predicting microcircuit connectivity and for setting up simulations using the NEURON simulation environment in a reproducible way. We also illustrate how to further 'curate' data on single neuron morphologies acquired from public databases. This model building pipeline was used to set up a first version of a full-scale cellular level model of mouse dorsal striatum. Model components from that work are here used to illustrate the different steps that are needed when modelling subcortical nuclei, such as the basal ganglia.

SUBMITTER: Hjorth JJJ

PROVIDER: S-EPMC8566446 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:To characterize each cognitive function per se and to understand the brain as an aggregate of those functions, it is vital to relate dozens of these functions to each other. Knowledge about the relationships among cognitive functions is informative not only for basic neuroscientific research but also for clinical applications and developments of brain-inspired artificial intelligence. In the present study, we propose an exhaustive data mining approach to reveal relationships among cognitive functions based on functional brain mapping and network analysis. We began our analysis with 109 pseudo-activation maps (cognitive function maps; CFM) that were reconstructed from a functional magnetic resonance imaging meta-analysis database, each of which corresponds to one of 109 cognitive functions such as 'emotion,' 'attention,' 'episodic memory,' etc. Based on the resting-state functional connectivity between the CFMs, we mapped the cognitive functions onto a two-dimensional space where the relevant functions were located close to each other, which provided a rough picture of the brain as an aggregate of cognitive functions. Then, we conducted so-called conceptual analysis of cognitive functions using clustering of voxels in each CFM connected to the other 108 CFMs with various strengths. As a result, a CFM for each cognitive function was subdivided into several parts, each of which is strongly associated with some CFMs for a subset of the other cognitive functions, which brought in sub-concepts (i.e., sub-functions) of the cognitive function. Moreover, we conducted network analysis for the network whose nodes were parcels derived from whole-brain parcellation based on the whole-brain voxel-to-CFM resting-state functional connectivities. Since each parcel is characterized by associations with the 109 cognitive functions, network analyses using them are expected to inform about relationships between cognitive and network characteristics. Indeed, we found that informational diversities of interaction between parcels and densities of local connectivity were dependent on the kinds of associated functions. In addition, we identified the homogeneous and inhomogeneous network communities about the associated functions. Altogether, we suggested the effectiveness of our approach in which we fused the large-scale meta-analysis of functional brain mapping with the methods of network neuroscience to investigate the relationships among cognitive functions.

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Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda.

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