BIRN – Biomedical Informatics Research Network

List of Data by Category

Human Functional Imaging Data

The following are large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

• BrainScape_BS002 – 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.

• BrainScape_BS003 – 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).

• fBIRN PhaseII – Neuroimaging Calibration Study (Phase II)

  The FBIRN multi-site dataset of subjects with schizophrenia and controls includes functional MRI images, behavioral data, demographic, and clinical assessments on 253 subjects from around the US.

• fBIRNTravelingSubject2003 – Traveling subjects study (Phase I)

  This dataset includes five healthy subjects imaged twice at each of ten FBIRN MRI scanners on successive days.

fMRI Calibration Data (Agar Phantom)

• FMRI Calibration Data (Agar Phantom QA)

  The FBIRN agar phantom is used regularly for Quality Assurance, to assess scanner stability.

Structural Brain Imaging Data

Researchers can use structural imaging data sets to discover correlations between the volume of certain brain structures and disease. The effects are usually subtle and large numbers of subjects are often needed to identify correlations. Several groups connected with BIRN have conducted such studies on populations throughout the adult age range and including specific disease populations. In addition, diffusion tensor imaging (DTI) is becoming an important part of structural imaging studies. With this technique, one can visualize tissue whose structure is ordered. One application is to study brain white matter, which consists of oriented fibers. BIRN also provides below a DTI data set from a single subject that can be used to build up data with increasing of signal-to-noise ratio or simply used as test data for processing or analysis software.

• Efficient Longitudinal Upload of Depression in the Elderly (ELUDE)

  The ELUDE dataset is a longitudinal study of late-life depression at Duke University.

• 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.

• Morphometry BIRN Multi-site Multi-session Structural MRI Data

  This data set consists of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems).

• Multisite Imaging Research In the Analysis of Depression (MIRIAD)

  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.

• Open Access Structural Imaging Series (OASIS)

  This set consists of a cross-sectional collection of 416 human subjects aged 18 to 96, including individuals with Alzheimer’s disease; T1-weighted MRI scans obtained in single scan sessions are included.

Cell Centered Database

• Cell Centered Database (CCDB)

  The CCDB is an Internet databases for cellular imaging data. The CCDB houses structural and protein distribution information derived from confocal, electron microscopy and multiphoton microscopy.

Mouse Atlases

MouseBIRN has made available several multimodal digital atlases:

• 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.

• EAE Mouse model of Multiple Sclerosis

  Multiple datasets for an Experimental Autoimmune Encephalitis (EAE) mouse model of Multiple Sclerosis.

• 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)).

• 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).

• Mouse 3D MR Neonatal (P0) atlas

  This atlas is reconstructed from T2-weighted magnetic resonance images acquired from 8 normal C57BL/6J neonatal mice.

• Mouse 3D Nissl Neonatal (P0) atlas

  This atlas is a reconstructed Nissl volume collected from a C57BL/6J neonatal mouse.

• 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.

• 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.

• Mouse Shiverer DTI high-resolution contrast-enhanced data

  Acquired from six background control (C3HeB) and six dysmyelinating shiverer (C3Fe.SWV shi/shi) mouse brains.

• 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).

• 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.