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About SPARC

  • What Can I Do with SPARC?
  • What is SPARC?
    • SPARC Portal Roadmap
    • SPARC Data and Resource Center Cores and Steering Committee
    • DAT-Core
    • K-Core
    • MAP-Core
    • SIM-Core
    • Key o²S²PARC features
    • DRC Open Office Hours
    • SPARC and Re3 Data
    • HEAL Initiative data on SPARC
  • In Silico Studies Roadmap
  • Glossary
  • Is SPARC HIPAA compliant?

SPARC Portal Features

  • SPARC Portal Overview
  • SPARC Portal Login
  • Gallery Viewer
  • Image Viewer
  • Integrated Maps Viewer
  • Scaffold Viewer
  • Segmentation Viewer
  • Simulation Viewer
  • Plot Viewer
  • Organ Scaffolds
  • Faceted Browse
  • SPARC Portal Known Issues

Contributing to SPARC

  • Submit to SPARC
  • SPARC Portal Data Repository Structure
  • Submission Walkthrough Intro
    • Create Your Protocol
    • Prepare Your Metadata Files
      • Prepare The Metadata File for Computational Datasets
    • Organize Your Files
    • Upload Your Data
  • FAQs: SPARC Data Submission
    • Guidelines for Effective SPARC Dataset Titles and Descriptions
    • Formatting SPARC Datasets
  • Uploading Files to the SPARC DAT-Core
  • User Accounts and Teams
  • Embargoed Datasets
  • Dataset Access Downloads Notification to Dataset Owners
  • What’s Your SPARC Story?
  • Data Sharing and Management Costs for NIH Grant Proposals
    • Publishing costs for the SPARC Portal

Using SPARC Datasets

  • Using SPARC Datasets
  • Navigating SPARC Datasets
  • Publishing a Flatmap as a SPARC Dataset
  • Citing SPARC Datasets and Models in Manuscripts
  • Citing a Dataset from the Manifest JSON file
  • SPARC Data and Usage Statistics
  • SPARC Dataset Citations
  • Tutorial: Running a Cardiovascular System Model on o²S²PARC from the SPARC Portal
  • Tutorial: Running ASCENT On o²S²PARC
  • Tutorial: Introduction To CAD Modeling On o²S²PARC
  • Tutorial: Running a MetaModeling Pipeline On o²S²PARC

Using SPARC Resources

  • SPARC Python Client
    • Tutorial: Download public data, scaffolds and run computations
    • Tutorial: Using sparc.client for data movement in SPARC
  • Accessing Public Datasets
  • Accessing SCKAN
  • Accessing Published o²S²PARC Simulations
  • Accessing public o²S²PARC Services
  • Using a Jupyter Notebook with SPARC data
  • SODA: Software to Organize Data Automatically
  • SciCrunch Vocabulary Services
  • SCKANNER
    • SCKANNER Tutorial
  • Introduction to Maps
  • Working with Multiple Views in Maps
  • SPARC Portal Map Annotation Tool
    • Tutorial: SPARC Portal Map Annotation Tool
  • How to Use the Sidebar in Maps
  • Scaffold Mapping Tools
    • Scaffold Mapping Tools: Installation Guide
    • Publishing Generic Organ Scaffold as a SPARC Dataset
    • Publishing Scaffold Maps as a SPARC Dataset
    • Tutorial: Scaffold Mapping Tools: Mapping Image Data
    • Tutorial: Scaffold Mapping Tools: Mapping Physiological Data
    • Tutorial: Scaffold Mapping Tools: Mapping Image Data From Flat Preparation
    • Scaffold Mapping Tools: Creating Skeleton Dataset Structure
    • Scaffold Mapping Tools: Annotation
    • Scaffold Mapping Tools: Adding Provenance
    • Scaffold Mapping Tools: Adding Fiducial Marker And Group
    • Scaffold Mapping Tools: Reusing Scaffolds
    • Tutorial: Scaffold Mapping Tools: Mapping Image Data v0.21.4
    • Scaffold Mapping Tools: Mapping Image Data v0.19.1
    • Scaffold Mapping Tools: Mapping Physiological Data v0.19.1
    • Scaffold Mapping Tools: Mapping Image Data From Flat Preparation v0.19.1
    • Scaffold Mapping Tools: Mapping Image Data v0.17.4
  • Documentation, Examples, and Software for SPARC Map Reuse
    • Anatomical Flatmap Resources
    • Tutorial: Discovering and reusing connectivity knowledge in flatmaps
  • Demo of Use of Segmentation Conversion Tools for Scaffold Mapping
  • Microfile+: Convert Microscopy Image Data and Metadata to SPARC Standard Formats
  • Functional Connectivity Map
  • SPARC Open Dataset Structure

Video Tutorials and Webinars

  • SPARC YouTube Channel
  • SPARC Portal Walkthrough
  • Intro to the New SPARC 2.0 Dataset Structure
  • Using AWS to Access Public Datasets
    • Setting up an AWS Account to Access Large SPARC Datasets
    • Using the AWS Command Line Interface to Access Large SPARC Datasets
  • Running JupyterLabs on SPARC Resources
  • Access o²S²PARC from the SPARC Portal
  • Mapping Data To Organ Scaffold
  • SPARC Webinars

For Developers and Data Analysts

  • Information for Developers
  • SPARC Platform Integrations
  • SPARC APIs and Open Access Code
  • Connecting MBF Bioscience Software to the Pennsieve Platform
  • FAIR Image Segmentation in MBF Bioscience Software
  • SPARC Portal Schema
  • How to Clean an ORCID Profile
  • SPARC Systems Status
  • Supported Browsers

Policies and Standards

  • SPARC Terms of Service
  • NIH SPARC Embargoed Data Use Agreement
  • SPARC Dataset Structure (SDS)
  • SPARC Material Sharing Policy
  • SPARC Standards Process (NEW 2024)
  • SPARC DRC Privacy Policy
  • SPARC Governance Regulations
  • SPARC DRC Operation
  • SPARC Anatomical Working Group (SAWG)
  • Standards
  • Ontologies
  • Promotional Resources
  • Sustainable SPARC
  • SPARC Data Persistence Policy
  • SPARC Changes to Published Datasets Policy
    • List of SPARC Datasets Removed from the SPARC Portal
  • File Formats Accepted by SPARC

Feedback

  • Suggest Edits and Content - DRC Investigators
  • Suggest Edits and New Content - Visitors

Newsletter

  • SPARC Plug Newsletter Archive
    • SPARC Plug Winter 2025
    • SPARC Plug Autumn 2024
    • SPARC Plug Summer 2024
    • SPARC Plug Spring 2024
    • SPARC Plug Winter 2024
    • SPARC Plug Autumn 2023
    • SPARC Plug Summer 2023
    • SPARC Plug Spring 2023
    • SPARC is now an Open Data Repository
    • SPARC Plug Autumn 2022
    • SPARC hits major dataset milestone
    • SPARC Plug Spring 2022
    • SPARC Plug Winter 2022
    • SPARC Plug Summer 2021
    • SPARC Plug Winter 2021
    • SPARC Plug Autumn 2020

Supported Consortia

  • NIH RE-JOIN Resource Page
  • NIH PRECISION Human Pain Network Resource Page
  • SPARC Resources List

Intro to the New SPARC 2.0 Dataset Structure

Video introducing SPARC's uniform file structure

Suggest Edits

Each SPARC dataset is curated to have a uniform file structure. The Intro to the New SPARC 2.0 Dataset Structure video introduces this structure.

Updated 12 months ago


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