Currently Available Data

The BDR is a sustainable archive of data generated by the biomedical research community. Data housed in the BDR are available for sharing and exchange. Biomedical imaging data from humans and animal models are the primary data type available for download with a minimal set of descriptive metadata, and in some cases, associated clinical, genetic, or other biomedical data.

Data will be discoverable via a concept-based query interface and further queried and explored via database-specific query interfaces. The integration of data across multiple sources and domains requires common vocabularies to locate relevant information, to associate similar data types, and to discover knowledge through a higher level semantic network. All data sources will be annotated using a common ontology, BIRNLex, to enable intelligent exploration of the BDR data resources.

BIRN DATA REPOSITORY SOURCES:

Human Imaging Database (HID)

  • Human Functional MRI data: Traveling subjects study: This dataset includes five healthy subjects imaged twice at each of ten FBIRN MRI scanners on successive days. Functional and structural imaging, behavioral, and demographic data are available from 100 scanning sessions on these subjects.
  • BrainScape Resting State fMRI Dataset 1: This dataset includes seventeen healthy subjects with four resting state fixation scans plus one T1 scan and one T2 scan. The data were collected as part of a study on the behavioral effects of spontaneous BOLD fluctuations.
  • BrainScape Resting State fMRI Dataset 2: This dataset includes ten healthy subjects scanned 3 times with 3 conditions: eyes open, eyes closed, and fixating in addition to two anatomical scans (T1 and T2).

XNAT

  • OASIS : Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults: This set consists of a cross-sectional collection of 416 subjects aged 18 to 96, including individuals with Alzheimer's disease; T1-weighted MRI scans obtained in single scan sessions are included. Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.
  • MIRIAD : Multisite Imaging Research In the Analysis of Depression: A multiple institution study of structural MRI, including raw PD and T2 MRIs and derived measures of white matter changes, basal ganglia and other regions. Demographic and extensive clinical assessment data is available for each case.
  • MorphDTI_p0001 : High SNR Healthy Volunteer DTI Calibration Dataset at 1.5T: This dataset contains the acquired DTI data and the co-registered DTI data for a healthy male volunteer scanned on three separate scanning sessions over 2 days. This large dataset (45 DTI scans) can be used as a reference for DTI data on a 1.5 T scanner to validate analysis methods and calibrate the SNR requirements and acquisition schemes of multi-site DTI imaging studies.
  • ELUDE : Efficient Longitudinal Upload of Depression in the Elderly: The ELUDE dataset is an anonymized collection of a longitudinal study of late-life depression at Duke University. There are 281 depressed subjects and 154 controls included. An MR scan of each subject was obtained every 2 years for up to 8 years (total of 1093 scans). Clinical assessments occurred more frequently and consists of a battery of psychiatric tests including several depression-specific tests.

Cell Centered Data Base (CCDB)

  • The Cell Centered Database (CCDB) contains high resolution 2D, 3D, and 4D data from light and electron microscopy from the nervous system and other systems.

Microarray Database

  • Through the Mouse BIRN Atlasing Toolkit (MBAT), it is possible to access processed microarray data from multiple experiments and data sources. This data covers several strains, developmental stages, and non-neural data.

Mouse BIRN Atlases


CURRENTLY AVAILABLE DATA FROM BIRN-ENABLED COLLABORATIONS:

Human Functional MRI data: Traveling subjects study. The Function BIRN Phase I Traveling Subjects Dataset includes five subjects who traveled the country and were imaged twice at each of ten FBIRN site on successive days. Functional and structural imaging, behavioral, and demographic data are available from 100 scanning sessions on these subjects. [Function BIRN]

Human structural magnetic resonance imaging (MRI) data, cross-sectional. Single-site series of structural MRI data sets from 416 subjects across the adult life span, including healthy individuals and individuals with dementia of the Alzheimer's type. [Open Access Structural Imaging Series (OASIS). D. Marcus, Washington University, R. Buckner, Harvard University].

Mouse MDA: Non-human, Mouse 3D MR minimum deformation atlas. This atlas is constructed from T2-weighted magnetic resonance microscopy (MRM) images acquired from 11 normal female C57BL/6J mice and is the default atlas for the Mouse BIRN Atlasing Toolkit (MBAT).

MPTP Model: Non-human, Mouse MPTP model of Parkinson's Disease microarray dataset. Six treat and 6 normal mice from this experiment are shared on the BIRN Microarray Database and may be queried and visualized in the Mouse BIRN Atlasing Toolkit (MBAT).

Non-human, magnetic resonance microscopy (MRM) study of the Reeler mouse brain. This has been proposed as a model for schizophrenia, bipolar disorder, autism, and lissencephaly [A. Badea; Duke University].

Non-human, multiphoton micrographs of the cerebellum of C57BL/6H normal mouse. These data provide a high resolution, large scale mosaic image of a cerebellar distribution of cell bodies and alpha-synuclein from a non-transgenic animal [M. Martone; UCSD].

Non-human, Mouse 3D Atlas based on a magnetic resonance microscopy (MRM) image. Acquired from a normal, 100-day old male C57BL/6J mouse, the atlas is comprised of a diffusion-weighted image volume, a label volume, a mask volume, and a label index. [BIRN Atlas Tool (MBAT) or (SHIVA)].

Non-human, Mouse Diffusion Tensor Imaging (DTI) Atlas of developing mouse brains. Embryonic and adult mouse brain images were acquired using three dimensional diffusion tensor magnetic resonance microimaging technique.

Non-human, Mouse Shiverer DTI high-resolution contrast-enhanced data. Acquired from six background control (C3HeB) and six dysmyelinating shiverer (C3Fe.SWV shi/shi) mouse brains.

Non-human, Mouse Common Specimen. Imaging a single fixed specimen using MRM from Duke's CIVM, Diffusion Weighted MR from Caltech's Beckman Institute, and Optical Histology and Staining from UCLA's LONI. UCSD's NCMIR performed Multiphoton Microscopy using tissue from an animal of the same strain.

Non-human, Duke Center for In-Vivo Microscopy (CIVM) High Resolution MRI Images. Duke Center for In-Vivo Microscopy (CIVM) contains high resolution MR brain images of normal and human-disease-model mice, including multiple MRI modalities and structural segmentation.

Mouse MR Neonatal: Non-human, Mouse 3D MR Neonatal (P0) atlas. This atlas is reconstructred from T2-weighted magnetic resonance images acquired from 8 normal C57BL/6J neonatal mice.

Mouse Nissl Neonatal: Non-human, Mouse 3D Nissl Neonatal (P0) atlas. This atlas is a reconstructed Nissl volume collected from a C57BL/6J neonatal mouse.

Mouse: Non-human, EAE Mouse model of Multiple Sclerosis. Multiple datasets for an Experimental Autoimmune Encephalitis (EAE) mouse model of Multiple Sclerosis. .

Mouse: Non-human, Tet-off Amyloid Precursor Protein (APP) Transgenic Model. Dr. Joanna Jankowsky at Caltech has developed a Tet-off APP model, in which the expression of APP can be controlled with antibiotic treatment. These mice show several significant advantages for use as a model for Alzheimers.

Non-human, mouse microarray data. Through the Mouse BIRN Atlasing Toolkit (MBAT), it is possible to access processed microarray data from multiple experiments and data sources. This data covers several strains, developmental stages, and non-neural data.

Non-human, cellular and subcellular light and electron microscopy data. The Cell Centered Database (CCDB) contains high resolution 2D, 3D, and 4D data from light and electron microscopy from the nervous system and other systems.  It may be searched either through their web-interface or through MBAT.