arXiv subjects

Paul Tiesinga

Publications and source records attributed to Paul Tiesinga.

4 recordsLinked to original sources

arXiv2022

Recommendations for repositories and scientific gateways from a neuroscience perspective

Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular needs. INCF (International Neuroinformatics Coordinating Facility) has developed a set of recommendations and associated criteria for choosing or setting up and running a repository or scientific gateway, intended for the neuroscience community, with a FAIR neuroscience perspective. These recommendations have neurosciences as their primary use case but are often general. Considering the perspectives of researchers and providers of repositories as well as scientific gateways, the recommendations harmonize and complement existing work on criteria for repositories and best practices. The recommendations cover a range of important areas including accessibility, licensing, community responsibility and technical and financial sustainability of a service.

cs.CY↗

arXiv2017

Feeding the human brain model

The goal of the Human Brain Project is to develop during the next decade an infrastructure necessary for running a simulation of the entire human brain constrained by current experimental data. One of the key issues is therefore to integrate and make accessible the experimental data necessary to constrain and fully specify this model. The required data covers many different spatial scales, ranging from the molecular scale to the whole brain and these data are obtained using a variety of techniques whose measurements may not be directly comparable. Furthermore, these data are incomplete, and will remain so at least for the coming decade. Here we review new neuroinformatics techniques that need to be developed and applied to address these issues.

q-bio.QM↗

arXiv2014

The Scalable Brain Atlas: instant web-based access to public brain atlases and related content

The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays.

q-bio.NC↗

arXiv2005

Attentional modulation of firing rate and synchrony in a model cortical network

When attention is directed into the receptive field of a V4 neuron, its contrast response curve is shifted to lower contrast values (Reynolds et al, 2000, Neuron 26:703). Attention also increases the coherence between neurons responding to the same stimulus (Fries et al, 2001, Science 291:1560). We studied how the firing rate and synchrony of a densely interconnected cortical network varied with contrast and how they were modulated by attention. We found that an increased driving current to the excitatory neurons increased the overall firing rate of the network, whereas variation of the driving current to inhibitory neurons modulated the synchrony of the network. We explain the synchrony modulation in terms of a locking phenomenon during which the ratio of excitatory to inhibitory firing rates is approximately constant for a range of driving current values. We explored the hypothesis that contrast is represented primarily as a drive to the excitatory neurons, whereas attention corresponds to a reduction in driving current to the inhibitory neurons. Using this hypothesis, the model reproduces the following experimental observations: (1) the firing rate of the excitatory neurons increases with contrast; (2) for high contrast stimuli, the firing rate saturates and the network synchronizes; (3) attention shifts the contrast response curve to lower contrast values; (4) attention leads to stronger synchronization that starts at a lower value of the contrast compared with the attend-away condition. In addition, it predicts that attention increases the delay between the inhibitory and excitatory synchronous volleys produced by the network, allowing the stimulus to recruit more downstream neurons.

q-bio.NC↗