For AI agents: visit https://docs.sparc.science/v1.0/llms.txt for an index of all pages formatted in Markdown and endpoints in OpenAPI.

Jump to Content

Home All Help Articles Change logs

All Help Articles

SPARC Portal Homepage

Jump to Content

Home All Help Articles Change logs

These docs are for v1.0. Click to read the latest docs for v6.0.

About SPARC

What Can I Do with SPARC?
What is 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
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
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
Notice Regarding Repository Review in Response to Executive Order 14168

Feedback

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

Newsletter

SPARC Plug Newsletter Archive

Supported Consortia

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

Mapping Data To Organ Scaffold

Learn how to Map Data To Organ Scaffold

Updated about 1 year ago

Access o²S²PARC from the SPARC Portal

Did this page help you?

The open community platform for bridging the body and the brain through neuroscience and systems physiology data, computational and spatial modeling, and device design.

Learn More

About SPARC
Help Center
Funding Opportunities
NIH SPARC Program
SPARC Systems Status
SPARC Publications

Policies

Privacy Policy
Terms of Service
Overview of SPARC Policies

Help Us Improve

Site Feedback
Discussion Forum

Stay Up-to-Date

Join our E-mail list
SPARC BioRxiv