A comprehensive, FAIR file format for neuroanatomical structure modeling

Sullivan, A. E.; Tappan, Susan; Angstman, P. J.; Rodríguez, Alfredo; Thomas, G. C.; Hoppes, D. M.; Abdul-Karim, M. A.; Heal, Maci; Glaser, Jack R.

doi:10.1101/2020.09.22.306670

Cited by 3 publications

(2 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Segmented anatomical elements are written in MBF Bioscience's digital reconstruction file format. The format, in strides with SPARC's FAIR and open data objectives, is documented in the Neuromorphological File Specification and is publicly available 20 (Sullivan et al, 2020 ). A uniform data file format simplifies the registration procedure to a common coordinate space.…”

Section: Image Segmentation and Annotationmentioning

confidence: 99%

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

et al. 2021

View full text Add to dashboard Cite

The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.

show abstract

Section: Image Segmentation and Annotationmentioning

confidence: 99%

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Segmented anatomical elements are written in MBF Bioscience's digital reconstruction file format. The format, in strides with SPARC's FAIR and open data objectives, is documented in the Neuromorphological File Specification and is publicly available 24 (Sullivan et al, 2020). A uniform data file format simplifies the registration procedure to a common coordinate space.…”

Section: Image Segmentation and Annotationmentioning

confidence: 99%

The SPARC DRC: Building a resource for the autonomic nervous system community

Osanlouy

Bandrowski

Bono

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.

show abstract

Computational modelling of nerve stimulation and recording with peripheral visceral neural interfaces

et al. 2021

View full text Add to dashboard Cite

Objective. Neuromodulation of visceral nerves is being intensively studied for treating a wide range of conditions, but effective translation requires increasing the efficacy and predictability of neural interface performance. Here we use computational models of rat visceral nerve to predict how neuroanatomical variability could affect both electrical stimulation and recording with an experimental planar neural interface. Approach. We developed a hybrid computational pipeline, Visceral Nerve Ensemble Recording and Stimulation (ViNERS), to couple finite-element modelling of extracellular electrical fields with biophysical simulations of individual axons. Anatomical properties of fascicles and axons in rat pelvic and vagus nerves were measured or obtained from public datasets. To validate ViNERS, we simulated pelvic nerve stimulation and recording with an experimental four-electrode planar array. Main results. Axon diameters measured from pelvic nerve were used to model a population of myelinated and unmyelinated axons and simulate recordings of electrically evoked single-unit field potentials (SUFPs). Across visceral nerve fascicles of increasing size, our simulations predicted an increase in stimulation threshold and a decrease in SUFP amplitude. Simulated threshold changes were dominated by changes in perineurium thickness, which correlates with fascicle diameter. We also demonstrated that ViNERS could simulate recordings of electrically-evoked compound action potentials (ECAPs) that were qualitatively similar to pelvic nerve recording made with the array used for simulation. Significance. We introduce ViNERS as a new open-source computational tool for modelling large-scale stimulation and recording from visceral nerves. ViNERS predicts how neuroanatomical variation in rat pelvic nerve affects stimulation and recording with an experimental planar electrode array. We show ViNERS can simulate ECAPS that capture features of our recordings, but our results suggest the underlying NEURON models need to be further refined and specifically adapted to accurately simulate visceral nerve axons.

show abstract

A comprehensive, FAIR file format for neuroanatomical structure modeling

Cited by 3 publications

References 37 publications

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

The SPARC DRC: Building a resource for the autonomic nervous system community

Computational modelling of nerve stimulation and recording with peripheral visceral neural interfaces

Contact Info

Product

Resources

About