Sums:About

From Van Essen Lab

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
= About SumsDB =
= About SumsDB =
-
* SumsDB is a repository of brain-mapping data (surfaces & volumes; structural & functional data) from many laboratories.
+
[Image:SumsAboutImage.jpg]
-
* SumsDB features WebCaret for online visualization of SumsDB datasets.
+
 
 +
SumsDB (the Surface Management System DataBase) provides access to a growing body of neuroimaging and related data.  WebCaret software provides online data visualization for datasets in SumsDB.
 +
 
 +
== Five Main Categories of Data Based on Data Type and Usage ==
 +
 
 +
=== Atlas Datasets ===
 +
* surface and volume data
 +
* structural and functional data
 +
* data on cerebral cortex and cerebellar cortex
 +
* human data – normal and neurological/psychiatric disorders
 +
* nonhuman primate data: macaque, chimpanzee, gorilla
 +
* rodent: mouse and rat data
 +
 
 +
=== Searchable Stereotaxic Foci and fMRI Maps ===
 +
* published data, curated and customized for data mining
 +
* over 25,000 sterotaxic foci from nearly 1,000 published studies
 +
 
 +
=== Publication Associated Datasets ===
 +
* underlay key figures in specific online publications:
 +
* individual subject data and population data mapped to atlases
 +
 
 +
=== Project-Related Datasets ===
 +
* from various ongoing projects that serve archival purposes and sharing with selected collaborators
 +
* data from FreeSurfer, CIVET, and other brainmapping software besides Caret
 +
 
 +
=== Tutorials ===
 +
* documents and associated datasets from tutorials for both SumsDB/WebCaret and Caret.
 +
 
 +
== Data Access and Security ==
 +
* SumsDB provides multiple levels of data access and security
 +
* Free (public) access (e.g., for data associated with published studies)
 +
* Data access restricted to collaborators in different laboratories
 +
* Owner-only access for work in progress
 +
 
 +
=== Data Organization ===
 +
* Download data as individual files or as collections (‘spec files’) customized for offline analysis in Caret
 +
 
 +
== WebCaret ==
 +
* WebCaret provides online ‘Caret-style’ visualization without software or data downloads:
 +
* WebCaret ‘scenes’ facilitate rapid visualization of complex combinations of data
 +
* Bi-directional links between online publications and WebCaret/SumsDB provide:
 +
* Links from figures in online journal article to corresponding scenes in WebCaret
 +
* Links from metadata in WebCaret directly to relevant online publications and figures
 +
 
 +
== Searching and Data Mining ==
 +
* Searching and data mining options using SumsDB and WebCaret:
 +
* Search by data type, filename, associated metadata (text-based search)
 +
* Spatially based queries
 +
** proximity to stereotaxic coordinates
 +
** overlap with selected fMRI activations (metric files)
 +
** overlap with identified cortical areas (paint files)
 +
* Searches can be applied to:
 +
** currently loaded datasets
 +
** ‘processed’ datasets
 +
** all public SumsDB data
 +
** restricted access data   
 +
* Search results can be:                 
 +
** viewed in WebCaret                 
 +
** combined with other loaded data sets                 
 +
** downloaded directly
 +
 
 +
== Hardware == 
 +
 
 +
* SumsDB and WebCaret on a Linux cluster housed in the Electronic Radiology Laboratory in the Washington University Department of Radiology.  * * * Automatic data backup and recovery are handled through a Network Attached Storage system.

Revision as of 14:33, 18 November 2008

Contents

About SumsDB

[Image:SumsAboutImage.jpg]

SumsDB (the Surface Management System DataBase) provides access to a growing body of neuroimaging and related data. WebCaret software provides online data visualization for datasets in SumsDB.

Five Main Categories of Data Based on Data Type and Usage

Atlas Datasets

  • surface and volume data
  • structural and functional data
  • data on cerebral cortex and cerebellar cortex
  • human data – normal and neurological/psychiatric disorders
  • nonhuman primate data: macaque, chimpanzee, gorilla
  • rodent: mouse and rat data

Searchable Stereotaxic Foci and fMRI Maps

  • published data, curated and customized for data mining
  • over 25,000 sterotaxic foci from nearly 1,000 published studies

Publication Associated Datasets

  • underlay key figures in specific online publications:
  • individual subject data and population data mapped to atlases

Project-Related Datasets

  • from various ongoing projects that serve archival purposes and sharing with selected collaborators
  • data from FreeSurfer, CIVET, and other brainmapping software besides Caret

Tutorials

  • documents and associated datasets from tutorials for both SumsDB/WebCaret and Caret.

Data Access and Security

  • SumsDB provides multiple levels of data access and security
  • Free (public) access (e.g., for data associated with published studies)
  • Data access restricted to collaborators in different laboratories
  • Owner-only access for work in progress

Data Organization

  • Download data as individual files or as collections (‘spec files’) customized for offline analysis in Caret

WebCaret

  • WebCaret provides online ‘Caret-style’ visualization without software or data downloads:
  • WebCaret ‘scenes’ facilitate rapid visualization of complex combinations of data
  • Bi-directional links between online publications and WebCaret/SumsDB provide:
  • Links from figures in online journal article to corresponding scenes in WebCaret
  • Links from metadata in WebCaret directly to relevant online publications and figures

Searching and Data Mining

  • Searching and data mining options using SumsDB and WebCaret:
  • Search by data type, filename, associated metadata (text-based search)
  • Spatially based queries
    • proximity to stereotaxic coordinates
    • overlap with selected fMRI activations (metric files)
    • overlap with identified cortical areas (paint files)
  • Searches can be applied to:
    • currently loaded datasets
    • ‘processed’ datasets
    • all public SumsDB data
    • restricted access data
  • Search results can be:
    • viewed in WebCaret
    • combined with other loaded data sets
    • downloaded directly

Hardware

  • SumsDB and WebCaret on a Linux cluster housed in the Electronic Radiology Laboratory in the Washington University Department of Radiology. * * * Automatic data backup and recovery are handled through a Network Attached Storage system.
Personal tools
Sums Database