Available Data
BIRN TOOL IS UNDERGOING MAINTENANCE AND WILL NOT BE AVAILABLE TO DOWNLOAD DURING THE WEEK OF APRIL 6 - APRIl 10, 2009. PLEASE CHECK BACK LATER IN THE WEEK FOR ADDITIONAL INFORMATION AND UPDATES. WE APOLOGIZE FOR ANY INCONVENIENCE.
The BDR is a sustainable archive that facilitates the sharing and exchange of data generated by the biomedical research community. Biomedical imaging data from humans and animal models are the primary data type available with a minimal set of descriptive metadata, and in some cases, associated clinical, genetic, or other biomedical data. Data are available through BDR resources including a variety of searchable databases along with archived downloads. Future BDR releases will allow data discovery via a concept-based query interface.
All data are freely available to the public with the provision of an active e-mail address and acceptance of the standard BDR Data Use Agreement; this agreement will be required prior to data download. To bypass this requirement in the future when using this device, please enable cookies, which will save your original acceptance of the Agreement; or create your own personalized BDR Portal Account, where these provisions are agreed to at account registration.
Please consider sharing your own data, or data resulting from your use of downloaded data, through the BDR to extend and strengthen this collaborative environment.
BIRN DATA REPOSITORY SOURCES:
- Traveling subjects study (Phase I): 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.
- 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. Subjects were recruited locally, evaluated with a standardized clinical assessment battery, and scanned twice at each of the 9 participating FBIRN sites. A standard FBIRN protocol was used for image acquisition with controlled variation at different sites and included a sensorimotor task (SM), an Auditory Oddball task (AO), a Serial Item Recognition Paradigm (SIRP), and a breathhold task (BH).
- 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).
- 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. Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.
- 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. Demographic and extensive clinical assessment data is available for each case.
- High SNR Healthy Volunteer DTI Calibration Dataset at 1.5T (MorphDTI_p0001): 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.
- Efficient Longitudinal Upload of Depression in the Elderly (ELUDE): The ELUDE dataset is 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.
- 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
- 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 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).
- 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].
- 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].
- 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 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 Shiverer DTI high-resolution contrast-enhanced data: Acquired from six background control (C3HeB) and six dysmyelinating shiverer (C3Fe.SWV shi/shi) mouse brains.
- 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.
- 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.
CURRENTLY AVAILABLE DATA FROM BIRN-ENABLED COLLABORATIONS:
- Neuroimaging Calibration Study (Phase II): Technological advances in functional and structural neuroimaging have revolutionized the biomedical investigation of neuropsychiatric illness. The tremendous potential that this methodology brings in advancing diagnostic and prognostic capabilities and in treatment of neuropsychiatric illness has a... More
- 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).
- Traveling subjects study (Phase I): 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.
- FMRI calibration data: The FBIRN agar phantom is used regularly for Quality Assurance, to assess scanner stability (as originally reported in Friedman L, Glover GH (2006) Report on a Multicenter fMRI Quality Assurance Protocol. /Journal of Magnetic Resonance in Imaging/, 23:827-839.). A single QA dataset consists of 200 regular EPI images collected with a flip angle of 77 degrees, and another 100 images with a flip angle of 10 degrees. The full information about the QA protocol is available here: https://xwiki.nbirn.net/xwiki/bin/view/Function-BIRN/FBIRN_Best_Practices . Data collected on FBIRN scanners since 2007 are publicly available here: http://www.nbirn.net/BIRN/cgi-bin/DataGrid/MRIs/publicMRIStability_post2007.cgi
- Open Access Structural Imaging Series (OASIS): 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].
- 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. Demographic and extensive clinical assessment data is available for each case.
- High SNR Healthy Volunteer DTI Calibration Dataset at 1.5T (MorphDTI_p0001): 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.
- Efficient Longitudinal Upload of Depression in the Elderly (ELUDE): The ELUDE dataset is 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.
- 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 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).
- 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].
- 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].
- 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 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 Shiverer DTI high-resolution contrast-enhanced data: Acquired from six background control (C3HeB) and six dysmyelinating shiverer (C3Fe.SWV shi/shi) mouse brains.
- 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.
- 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 3D MR Neonatal (P0)atlas: This atlas is reconstructred 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.
- EAE Mouse model of Multiple Sclerosis: Multiple datasets for an Experimental Autoimmune Encephalitis (EAE) mouse model of Multiple Sclerosis. .
- 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.
- 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.