Biomedical Informatics Research Network (BIRN) | Alphabetical List of Data

	Biomedical Informatics Research Network (BIRN) About About: Overview BIRN Video Introduction BIRN FAQs History Executive Committee Steering Committee Presentations/Papers Media Sponsors News Contact Us Capabilities Capabilities: Overview Demos and Downloads for Featured BIRN Capabilities Current Capabilities Working with BIRN Working with BIRN: Overview FAQ BIRN User Inquiry Working Groups Data Management Working Group Derived Data Working Group Genomics Working Group Information Integration Working Group Knowledge Engineering Working Group Operations Working Group Security Working Group Workflows Working Group Mailing Lists User Stories User Stories: Overview Multi-site fMRI Studies Resources Resources: Overview Tools Acquisition, Calibration and Quality Assurance Tools Analysis and Processing Tools Atlasing, Images and Visualization Tools Data Management and Collaboration Tools Ontologies, Standards and Terminologies Tools Security Tools Federated Informatics Research Environment (FIRE) Primer fMRI Scanner Calibration Methods and Recommendations fMRI Imaging Quality Assurance Methods Multi-site Cognitive Paradigms for fMRI studies Functional Imaging Calibration Paradigms All Tools Share Your Tools Software License Best Practices Supplemental Materials FBIRN Recommendations for Multi-Center fMRI Studies: Supplemental Material (JMRI cite) Supplement I: FBIRN Working Groups Supplement II: FBIRN Task presentation/psychometric collection Supplement III: FBIRN Scan parameters Supplement IV: FBIRN Quality Assurance Program Supplement V: FBIRN Informatics References Brain Morphometry Multi-site Studies Brain Morphometry Imaging Protocols Brain Morphometry MRI Phantom DTI Multisite Processing Functional MRI Multi-site Studies Data Alphabetical List of Data Collaborators Collaborators: Overview Radiation Oncology Pilot Project Taub Institute for Research at Columbia University Clinical Translational Science Institutes (CTSIs) Function BIRN Function BIRN Publications International Neuroinformatics Coordinating Facility (INCF) Cardiovascular Research Grid Alphabetical List of Data How to cite BIRN: If you use any of the following data for your project, please cite the appropriate NIH/NIGMS grant numbers in the Acknowledgement section of the manuscript: U24-RR021992 Function Biomedical Informatics Research Network (FBIRN) U24 RR021382 Morphometry Biomedical Informatics Research Network (MBIRN) U24-RR021760 Mouse Biomedical Informatics Research Network Each usage should also cite: U24 GM104203 Bio-Informatics Research Network Coordinating Center (BIRN-CC) Example: Some of the data used in this study was acquired through and provided by the Biomedical Informatics Research Network under the following support: U24-RR021992, Function BIRN (for functional data) and U24 GM104203, Bio-Informatics Research Network Coordinating Center (BIRN-CC). 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). 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. 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. Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) The ELUDE dataset is a longitudinal study of late-life depression at Duke University. fBIRN Phase 1 – Traveling subjects study This dataset includes five healthy subjects imaged twice at each of ten FBIRN MRI scanners on successive days. fBIRN Phase 2 – Neuroimaging Calibration Study 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. FMRI Calibration Data (Agar Phantom QA) The FBIRN agar phantom is used regularly for Quality Assurance, to assess scanner stability. 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). 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). 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. 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. Alphabetical List of Data BIRN Collaboration wiki BIRN Documentation wiki Presentations/Papers Project Management ACCESS Account Management Copyright Privacy Sitemap Contact Us BIRN is supported by NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.

Biomedical Informatics Research Network (BIRN) | Alphabetical List of Data

	Biomedical Informatics Research Network (BIRN) About About: Overview BIRN Video Introduction BIRN FAQs History Executive Committee Steering Committee Presentations/Papers Media Sponsors News Contact Us Capabilities Capabilities: Overview Demos and Downloads for Featured BIRN Capabilities Current Capabilities Working with BIRN Working with BIRN: Overview FAQ BIRN User Inquiry Working Groups Data Management Working Group Derived Data Working Group Genomics Working Group Information Integration Working Group Knowledge Engineering Working Group Operations Working Group Security Working Group Workflows Working Group Mailing Lists User Stories User Stories: Overview Multi-site fMRI Studies Resources Resources: Overview Tools Acquisition, Calibration and Quality Assurance Tools Analysis and Processing Tools Atlasing, Images and Visualization Tools Data Management and Collaboration Tools Ontologies, Standards and Terminologies Tools Security Tools Federated Informatics Research Environment (FIRE) Primer fMRI Scanner Calibration Methods and Recommendations fMRI Imaging Quality Assurance Methods Multi-site Cognitive Paradigms for fMRI studies Functional Imaging Calibration Paradigms All Tools Share Your Tools Software License Best Practices Supplemental Materials FBIRN Recommendations for Multi-Center fMRI Studies: Supplemental Material (JMRI cite) Supplement I: FBIRN Working Groups Supplement II: FBIRN Task presentation/psychometric collection Supplement III: FBIRN Scan parameters Supplement IV: FBIRN Quality Assurance Program Supplement V: FBIRN Informatics References Brain Morphometry Multi-site Studies Brain Morphometry Imaging Protocols Brain Morphometry MRI Phantom DTI Multisite Processing Functional MRI Multi-site Studies Data Alphabetical List of Data Collaborators Collaborators: Overview Radiation Oncology Pilot Project Taub Institute for Research at Columbia University Clinical Translational Science Institutes (CTSIs) Function BIRN Function BIRN Publications International Neuroinformatics Coordinating Facility (INCF) Cardiovascular Research Grid Alphabetical List of Data How to cite BIRN: If you use any of the following data for your project, please cite the appropriate NIH/NIGMS grant numbers in the Acknowledgement section of the manuscript: U24-RR021992 Function Biomedical Informatics Research Network (FBIRN) U24 RR021382 Morphometry Biomedical Informatics Research Network (MBIRN) U24-RR021760 Mouse Biomedical Informatics Research Network Each usage should also cite: U24 GM104203 Bio-Informatics Research Network Coordinating Center (BIRN-CC) Example: Some of the data used in this study was acquired through and provided by the Biomedical Informatics Research Network under the following support: U24-RR021992, Function BIRN (for functional data) and U24 GM104203, Bio-Informatics Research Network Coordinating Center (BIRN-CC). 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). 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. 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. Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) The ELUDE dataset is a longitudinal study of late-life depression at Duke University. fBIRN Phase 1 – Traveling subjects study This dataset includes five healthy subjects imaged twice at each of ten FBIRN MRI scanners on successive days. fBIRN Phase 2 – Neuroimaging Calibration Study 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. FMRI Calibration Data (Agar Phantom QA) The FBIRN agar phantom is used regularly for Quality Assurance, to assess scanner stability. 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). 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). 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. 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. Alphabetical List of Data BIRN Collaboration wiki BIRN Documentation wiki Presentations/Papers Project Management ACCESS Account Management Copyright Privacy Sitemap Contact Us BIRN is supported by NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.

Biomedical Informatics Research Network (BIRN) | Alphabetical List of Data

	Biomedical Informatics Research Network (BIRN) About About: Overview BIRN Video Introduction BIRN FAQs History Executive Committee Steering Committee Presentations/Papers Media Sponsors News Contact Us Capabilities Capabilities: Overview Demos and Downloads for Featured BIRN Capabilities Current Capabilities Working with BIRN Working with BIRN: Overview FAQ BIRN User Inquiry Working Groups Data Management Working Group Derived Data Working Group Genomics Working Group Information Integration Working Group Knowledge Engineering Working Group Operations Working Group Security Working Group Workflows Working Group Mailing Lists User Stories User Stories: Overview Multi-site fMRI Studies Resources Resources: Overview Tools Acquisition, Calibration and Quality Assurance Tools Analysis and Processing Tools Atlasing, Images and Visualization Tools Data Management and Collaboration Tools Ontologies, Standards and Terminologies Tools Security Tools Federated Informatics Research Environment (FIRE) Primer fMRI Scanner Calibration Methods and Recommendations fMRI Imaging Quality Assurance Methods Multi-site Cognitive Paradigms for fMRI studies Functional Imaging Calibration Paradigms All Tools Share Your Tools Software License Best Practices Supplemental Materials FBIRN Recommendations for Multi-Center fMRI Studies: Supplemental Material (JMRI cite) Supplement I: FBIRN Working Groups Supplement II: FBIRN Task presentation/psychometric collection Supplement III: FBIRN Scan parameters Supplement IV: FBIRN Quality Assurance Program Supplement V: FBIRN Informatics References Brain Morphometry Multi-site Studies Brain Morphometry Imaging Protocols Brain Morphometry MRI Phantom DTI Multisite Processing Functional MRI Multi-site Studies Data Alphabetical List of Data Collaborators Collaborators: Overview Radiation Oncology Pilot Project Taub Institute for Research at Columbia University Clinical Translational Science Institutes (CTSIs) Function BIRN Function BIRN Publications International Neuroinformatics Coordinating Facility (INCF) Cardiovascular Research Grid Alphabetical List of Data How to cite BIRN: If you use any of the following data for your project, please cite the appropriate NIH/NIGMS grant numbers in the Acknowledgement section of the manuscript: U24-RR021992 Function Biomedical Informatics Research Network (FBIRN) U24 RR021382 Morphometry Biomedical Informatics Research Network (MBIRN) U24-RR021760 Mouse Biomedical Informatics Research Network Each usage should also cite: U24 GM104203 Bio-Informatics Research Network Coordinating Center (BIRN-CC) Example: Some of the data used in this study was acquired through and provided by the Biomedical Informatics Research Network under the following support: U24-RR021992, Function BIRN (for functional data) and U24 GM104203, Bio-Informatics Research Network Coordinating Center (BIRN-CC). 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). 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. 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. Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) The ELUDE dataset is a longitudinal study of late-life depression at Duke University. fBIRN Phase 1 – Traveling subjects study This dataset includes five healthy subjects imaged twice at each of ten FBIRN MRI scanners on successive days. fBIRN Phase 2 – Neuroimaging Calibration Study 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. FMRI Calibration Data (Agar Phantom QA) The FBIRN agar phantom is used regularly for Quality Assurance, to assess scanner stability. 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). 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). 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. 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. Alphabetical List of Data BIRN Collaboration wiki BIRN Documentation wiki Presentations/Papers Project Management ACCESS Account Management Copyright Privacy Sitemap Contact Us BIRN is supported by NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.