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Welcome to SPARC
What is SPARC?
Why SPARC?
SPARC is an Open Data Repository
Submit to SPARC
Data Sharing and Management Costs for NIH Grant Proposals
Publishing costs for the SPARC Portal
Is SPARC HIPAA Compliant?
Sustainable SPARC
What Can I Do with SPARC?
Finding and Using Data
SPARC Portal Overview
SPARC Infrastructure
SPARC Portal Data Repository Structure
APIs and Open Access Code
SPARC Portal Schema
SPARC Systems Status
Data & Models
Navigating Datasets on SPARC
Anatomical Models: Organ Scaffolds
Viewers
Gallery Viewer
Image Viewer
Integrated Maps Viewer
Plot Viewer
Scaffold Viewer
Segmentation Viewer
Simulation Viewer
SPARC dataset (SDS) Viewer
Video Viewer
Data Re-Use
SPARC Open Dataset Structure
Public Datasets Download and Access
Embargoed Datasets
o²S²PARC Services
o²S²PARC Simulations
MAP Re-Use
Organ Scaffold Maps
Create your own visualization
Citing Datasets & Resources
Citing SPARC Datasets and Models in Manuscripts
Citing a Dataset from the Manifest JSON file
Measuring Re-use
SPARC Python Client
SPARC Portal Login
Portal Development
SPARC Portal Known Issues
Supported Browsers
SPARC Apps
SPARC Apps Overview
MAPs
Flatmaps
AC Flatmap Viewer
Controls
Sidebar in Maps
FC Flatmap Viewer
Controls
3D Whole Body Map
Controls
Multiple Views in Maps
MAP Tools Resource Page
o2S2PARC
Key o²S²PARC features
SCKANNER
Contributing Data & Models
Submission Overview
Getting Ready to Submit
Defining your SPARC Dataset or Model
Formatting SPARC Datasets
SPARC Workspace on Pennsieve
Best Practices
Guidelines for Effective SPARC Dataset Titles and Descriptions
Subjects, Samples, and Identifiers
Protocol Best Practices
Data Upload Best Practices
Submit: Submission Walkthrough
Create Your Protocol
Prepare Your Metadata Files
Publishing Generic Organ Scaffold as a SPARC Dataset
Publishing Scaffold Maps as a SPARC Dataset
Computational Models
Organize Your Files
Upload Your Data
Share Your Dataset with Curation
FAQs: SPARC Data Submission
Protocol FAQs
Data Upload FAQs
Review: Formal Curation/Request to Publish
Curation Resource Compendium
Tools & Resources
Tools & Resources Overview
Flatmap Resources
Flatmap Source Files
Connectivity Knowledge
Mapmakr
Flatmap Server
Flatmap Viewer
Map-Tools
Image Segmentation
FAIR Image Segmentation in MBF Bioscience Software
Connecting MBF Bioscience Software to the Pennsieve Platform
Demo of Use of Segmentation Conversion Tools for Scaffold Mapping
Map Annotation Tool
Microfile+
Scaffold Mapping Tools
Installation Guide
Creating a Skeleton Dataset Structure
Annotating in the Scaffold Mapping Tool
Adding Provenance
Adding Fiducial Markers and Groups
SciCrunch Vocabulary Services
SCKAN
Accessing SCKAN
SODA: Software to Organize Data Automatically
Learning Center
Learning Center Overview
DRC Open Office Hours
SPARC Portal Walkthrough
SPARC Tutorials
Discovering and reusing connectivity knowledge in flatmaps
Using a Jupyter Notebook with SPARC data
Mapping Image Data Demonstration Overview
Scaffold Mapping Tools: Mapping Image Data
Scaffold Mapping Tools: Mapping Physiological Data
Scaffold Mapping Tools: Mapping Image Data From Flat Preparation
SPARC Portal Map Annotation Tool
Publishing a Flatmap as a SPARC Dataset
Using sparc.client for data movement in SPARC
Download public data, scaffolds and run computations
SCKANNER Tutorial
Running a MetaModeling Pipeline On o²S²PARC
Introduction To CAD Modeling On o²S²PARC
Running ASCENT On o²S²PARC
Running a Cardiovascular System Model on o²S²PARC from the SPARC Portal
Tutorial Archive
Scaffold Mapping Tools: Mapping Image Data v0.17.4
Scaffold Mapping Tools: Mapping Image Data v0.19.1
Scaffold Mapping Tools: Mapping Image Data v0.21.4
Scaffold Mapping Tools: Mapping Physiological Data v0.19.1
Scaffold Mapping Tools: Mapping Image Data From Flat Preparation v0.19.1
SPARC Webinars
SPARC YouTube Channel
Intro to the New SPARC 2.0 Dataset Structure
Using AWS to Access Public Datasets
Access o²S²PARC from the SPARC Portal
Running JupyterLabs on SPARC Resources
Mapping Data To Organ Scaffold
Community & Collaborations
The SPARC Community
HEAL Initiative data on SPARC
What’s Your SPARC Story?
Projects
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
Promotional Resources
Governance & Standards
Governance
SPARC DRC Operation
SPARC Anatomical Working Group (SAWG)
Steering Committee
SPARC Data and Resource Center Structure
Data Coordination (DAT-Core)
Curation and Knowledge Management (K-Core)
MAP Synthesis (MAP-Core)
Modeling and Simulation (SIM-Core)
In Silico Studies Roadmap
Policies
Changes to Published Datasets Policy
List of SPARC Datasets Removed from the SPARC Portal
Data Persistence Policy
Embargoed Data Use Agreement
Material Sharing Policy
Notice Regarding Repository Review EO 14168
Portal Privacy Policy
Terms of Service
Standards
SPARC is FAIR
SPARC and Re3 Data
Standards Process
SPARC Dataset Structure (SDS)
Structured Folders and Metadata Files
SDS Versions
SDS Tools
Metadata Standards
Minimal Information Standard (MIS)
cMIS
Optical Microscopy Imaging
Naming Requirements
File Formats Accepted by SPARC
Ontologies
Protocols
Consortia Resources
NIH PRECISION Human Pain Network Resource Page
NIH RE-JOIN Resource Page
SPARC Resources List
Suggest
SCKANNER is a web-based software tool developed by the UCSD FDI lab and MetaCell to explore the current contents of SCKAN, a semantic store housing a comprehensive knowledge base of autonomic nervous system (ANS) and peripheral nervous system (PNS) nerve to end organ connectivity. Connectivity information is derived from SPARC experts, SPARC data, literature and textbooks. SCKAN supports reasoning and offers powerful query and visualization capabilities. Visit the Beta version of the tool at https://sckanner.stage.metacell.us/
