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What Can I Do with SPARC?

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Overview

SPARC is creating an open community platform for bridging the body and the brain through neuroscience and systems physiology data, computational and spatial modeling, and device design. SPARC is supported by the NIH Common Fund to provide a scientific and technological foundation for future bioelectronic medicine devices and protocols. Learn more about SPARC.

SPARC Portal Walkthrough

Take a walkthrough of the SPARC Portal to learn how to access high-quality multimodal, multi-species data and powerful tools for exploring the organization and function of PNS-end organ interactions. Through the portal, users can search, browse, view, and download datasets.

But SPARC does more, linking these data to 2D interactive maps where you can explore these data in the context of PNS connections, or view spatial distributions of cells and nerve processes within 3D computational scaffolds.

These 3D scaffolds are available for download along with tools. The SPARC Portal provides access to the powerful o²S²PARC simulation platform, where you can run and tune dynamic models of PNS function, or create your own simulations.

Example: How can I use SPARC to understand the structure and function of the vagus nerve?

(See also: Using computers to simulate, optimize, and understand neural responses to electrical signals to treat disease by SPARC investigator Nikki Pelot.)

NameLink
Access and explore anatomical multi-species datasets on the vagus nerveAnatomical dataset
Access and explore functional multi-species datasets on the vagus nerveFunctional dataset
Explore connections of the vagus nerveExample dataset

SPARC Flatmap
Predict parameter-dependent vagal nerve responses using an AI-informed computational model running on OSPARCPredict parameter-dependent vagal nerve responses
Use a Jupyter Notebook with SPARC datatutorial

You can also browse our YouTube tutorials to learn more about what SPARC offers. For help with our more advanced features, we suggest contacting us. For more information on the SPARC Data and Resource Center, which oversees development of the portal, see here.

View high-resolution images and movies

The SPARC Portal provides viewers for different data types that let you explore and view data through the portal without downloading the files.

Here we demonstrate how to view 2D and 3D microscopic images and movies through the Portal.

Example 1: iWAT (inguinal White Adipose Tissue) sympathetic innervation circuit pseudorabies viral tracing in reporter mice contributed by Muenzberg et al. (2021) DOI: 10.26275/mhq6-csy1

Example 2: Visualizing sympathetic projections in the intact brown adipose tissue depot in the mouse contributed by Seoeun Lee and Lori Zeltser (2020) DOI: 10.26275/ge74-ypxd

  • View a movie of sympathetic innervation of brown adipose tissue using confocal microscopy with iDISCO prepared tissue.

  • How do I do this myself? Movies can be viewed in two ways depending on the format. All .mp4 movies may be viewed through the File tab; other formats are sometimes made available through the Gallery Viewer). For the dataset, above, select the File tab for this dataset, and click the icon indicated below to view this movie.

File browser for above dataset.

File browser for above dataset. If a viewer is available for a data type (e.g., mp4 horizontal arrow), it is indicated by the icon in the Action column (slanted arrow)

View 2D and 3D maps of the autonomic nervous system

SPARC Maps offers a visual interface for exploring SPARC data and tools in the context of knowledge about ANS connectivity and provides 3D organ scaffolds for mapping the 3D distribution of ANS axons and cells. View tutorials on MAP Viewer and the 3D Scaffold Viewer.

Example 1: Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies by Hanna et al. (2021) DOI:10.26275/0ce8-cuwi.

  • View a 3D mapping of the parasympathetic innervation of the heart on a 3D SPARC organ scaffold.

  • How do I do this myself? To view data mapped onto scaffolds, select the "derivatives" folder under the File menu, and look for the folder labeled "Scaffolds." Look for the eye icon in the action menu.

SPARC provides access to multiple tools for creating scaffolds and mapping data to them. For more information, contact [email protected].

  • Access 3D organ scaffolds: Select the "Scaffold" facet under the "Models and Simulations" Tab.
  • Access 3D scaffold tools for fitting data and making scaffolds: Search for "scaffold" in our Tools and Resources catalog.

Access large-scale data in a scalable way

All datasets on the SPARC portal are directly accessible to the research community. Users can download datasets directly from the SPARC portal, or access the data on AWS for large-scale downloads and/or cloud-based analytics.

Each dataset is highly curated in accordance with all FAIR principles of data sharing. Check out documentation to access data in AWS to find out how to start accessing SPARC data in the cloud.

Create advanced analytic pipelines

The SPARC portal provides access to the o²S²PARC simulation platform, a cloud-based platform for developing, running, and sharing computational models and data analysis pipelines. Through the SPARC Portal, any user can directly investigate a contributed simulation through a “Run Simulation” link. Registered users with an o²S²PARC account have access to greater functionality such as editing existing simulation workflows and creating their simulations.

Examples of contributed simulations with detailed tutorials available on o²S²PARC
To run each simulation, click the "Run Simulation" button under the thumbnail image. See the abstract for details about model and access to a detailed tutorial on o²S²PARC.

Updated about 2 months ago

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