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Tools for Federation of Brain Data: The Cell Centered Database and BIRN projects. Maryann E. Martone, Ph. D. National Center for Microscopy and Imaging Research Center for Research in Biological Systems University of California, San Diego. Increasing Access to Data.

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slide1

Tools for Federation of Brain Data: The Cell Centered Database and BIRN projects

Maryann E. Martone, Ph. D.

National Center for Microscopy and Imaging Research

Center for Research in Biological Systems

University of California, San Diego

increasing access to data
Increasing Access to Data

The Cell Centered Database

Make 3D microscopic data available to the scientific community

  • High resolution light and electron microscopy
  • Link data obtained at cellular and subcellular scale to molecular and higher order structure
  • Most of our data is neural but data model is generic
  • Built on the BIRN infrastructure

http://ccdb.ucsd.edu

the ccdb
Research prototype for imaging information

Advanced features for representation and querying content of cell level data

Venue for sharing cell level 3D microscopic data

Data sets from tomography and correlated microscopy are made freely available to the scientific community

Imaging management system for microscopy data

Detailed data model for tracking and managing imaging data

Part of BIRN database federation

NCMIR’s contribution to Mouse BIRN

The CCDB
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tilt

mosaic

LM

time

EM

serial

survey

Project

  • Over 80 tables
  • Public, semi-public and private security levels

Experiment

Overview of CCDB Schema

Subject

Methodological characterization

Tissue

Product

Tissue

Processing

Fixation

Protein

Localization

Staining

Embedding

Anatomical

Details

Microscopy

Product

Microscopy

Image Details

Region of

Interest

Reconstruction

Image Details

Reconstruction

Segmentation

Tree Tracing

Morphometrics

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Smart Atlas: A GIS-based system for multiscale integration and query. Haiyun He, Joshua Tran, Ilya Zaslavsky

where is the cell in the ccdb
Where is the “Cell” in the CCDB?
  • CCDB is a “primary data” base not a “knowledge” base
  • Data model was elaborated around the techniques used to acquire images
  • Correlations between subcellular and cellular structure
  • Current view on web page is administrative/methodological
  • “Cell Centered Views” are being constructed through ontologies, the creation of cell-level atlases for classes of neurons and the creation of new data types for cell morphology
data types for neuronal data
Data Types for Neuronal Data

Shenglan Zhang, Yujun Wang, Amarnath Gupta

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National Center for Research Resources

  • Establish cyberinfrastructure for storing, manipulating and sharing data and resources
    • High speed, robust connectivity via Internet2
    • Data and computational resources
  • Current test beds focused on neuroimaging
    • Human MRI
    • Human fMRI
    • Mouse models of neurological disease
  • *Will no longer matter where data, instruments and computational resources are located physically”

BIRNBiomedical Informatics Research Network

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Duke

Database Mediation for BIRN

Find animal models of movement disorders where the volume of

basal ganglia structures are decreased and where loss of spines

from medium spiny neurons is observed.

Integrated

View

Knowledge Sources

Integrated

View Definition

Mediator

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UCSD

UCLA

Cal Tech

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Mediator

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Duke

UCLA

Cal Tech

The Smart Atlas: A Grid-based GIS tool for spatial integration of multiscale distributed brain data

Ilya Zaslavsky, Joshua Tran, Haiyun He, Amarnath Gupta

SRB

UCSD

slide18

Know Me Ontology Browser

Smart Atlas

Integration Engines

Spatial and Semantic Mark up

Data

BAMS

Knowledge

Web Forms

Genomic Data

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Planned Enhancements

  • Populate the database
    • Electronic lab notebooks --> CCDB using XML
  • Implement additional annotation capabilities
  • Implement new data types
  • Create advanced queries based on new data types and ontologies
  • Develop APIs and other aids to interoperability
  • Facilitate use of data in CCDB to aid in model construction (XML output)
  • Revision of CCDB schema
  • Continued Research:
    • Cell atlases
    • Ontologies for subcellular data
querying spatially distributed signals
Querying Spatially Distributed Signals

Spatial Histogram: Yujun Wang, Simone Santini, Amarnath Gupta