BIRN – Biomedical Informatics Research Network

Tools

This section includes a catalog of various tools made available through BIRN – these are tools developed and used in the BIRN community that others in the biomedical community may find helpful for their projects. These tools range from data sharing and user authentication tools to domain tools developed by the BIRN testbeds. Many of the following tools are made available through NITRC:

We’ve listed tools by the following general categories (you can also see a strictly alphabetized list of tools):

Acquisition, Calibration and Quality Assurance
Data Upload, Storage and Management
Data Sharing and Collaboration
Image Database Access
Analysis and Processing
Visualization and Atlasing
Security
Standards, Terminologies & Ontologies
Collaboration Services

List of Tools by Category

Acquisition, Calibration and Quality Assurance

B0 and Eddy Current Correction Code for Diffusion MRI
Software tool (executable plus code) and recommendations for acquisition protocols to correct distortions in diffusion MR images generated by main magnetic field inhomogeneities and eddy currents.
DTI Gradient Table Creator
DTI Gradient Table Creator computes the correct gradient table (i.e., the list of vectors that describe the diffusion weighting directions to use for analysis) for DTI acquisitions on Philips MRI scanners.
EPrime Phase II
These are E-prime programs for presenting stimuli to, collecting responses, and analyzing behavior from subjects.
Eprime Programs from Function BIRN Phase I Traveling Subjects
Employed during the FBIRN traveling subjects’ study of 2003, this is a Function-BIRN led study to standardize and calibrate imaging data for multi-site MRI studies by examining the brains of five subjects at nine different scanning sites across America.
Function BIRN Stability Phantom QA Procedures
Used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans.
Gradient non-linearity distortion correction
The goal of this software is to provide a 3D correction of image distortions in MRI data due to non-linearity of the magnetic fields from the imaging gradient coils.

Data Upload, Storage and Management

BXH/XCEDE Tools
A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.
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.
Clinical Assessment Layout Manager (CALM)
Helps incorporate online clinical assessment entry forms.
GridFTP
GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks.
Human Imaging Database (HID) System
Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities.
NeuroLex (formerly BIRNLEX)
NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.
XML-Based Clinical Experiment Data Exchange Schema (XCEDE)
Provides an extensive metadata hierarchy for describing and documenting research and clinical studies.
XNAT
The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data.

Data Sharing and Collaboration

BIRN_ID Generator
The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment.
BXH/XCEDE Tools
A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.
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.
Clinical Assessment Layout Manager (CALM)
Helps incorporate online clinical assessment entry forms.
Defacer for Structural MRI
This algorithm, which is still under the validation phase, locates the subject’s facial features and removes them without disturbing brain tissue.
Federated Informatics Research Environment (FIRE)
FIRE (coming in 2010) is an integrated suite of tools to put your data on a gridFTP set of servers, link it to a database which is automatically federated, to be able to retrieve it from multiple sites, with the data wrapped in XCEDE (XML) wrappers.
Human Imaging Database (HID) System
Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities.
NeuroLex (formerly BIRNLEX)
NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.
XNAT
The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data.

Image Database Access

Automated Image Registration (AIR)
A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.
BrainSuite
BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.
LONI Debabler
The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats.
LONI Inspector
The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.
LONI Provenance Editor
The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.
LONI Visualization Tool (LOVE)
An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.
Mouse BIRN Atlasing Toolkit (MBAT)
MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.
Registration using Embedded Maps (REM)
REM registers N-D image pairs that may contain topological differences.

Analysis and Processing

BXH/XCEDE Tools
A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.
CATNAP
CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program) is an end-to-end data processing pipeline for Philips PAR/REC Magnetic Resonance data files.
DTI Gradient Table Creator
DTI Gradient Table Creator computes the correct gradient table (i.e., the list of vectors that describe the diffusion weighting directions to use for analysis) for DTI acquisitions on Philips MRI scanners.
FBIRN Image Processing Scripts
FIPS is a package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control.
FreeSurfer
Set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface.
LONI Pipeline
Provides a visual programming interface that allows researchers to link many independently developed analysis programs into a processing “pipeline.”
XCEDE SPM Toolbox
Captures the results from activation maps using the XCEDE schema.

Visualization and Atlasing

3D Slicer
Open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data.
Automated Image Registration (AIR)
A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.
BrainSuite
BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.
LONI Debabler
The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats.
LONI Inspector
The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.
LONI Provenance Editor
The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.
LONI Visualization Tool (LOVE)
An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.
Mouse BIRN Atlasing Toolkit (MBAT)
MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.
MRI Studio
MRI Studio is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration.
Registration using Embedded Maps (REM)
REM registers N-D image pairs that may contain topological differences.

Security

GAMA
Grid Account Management Architecture, GAMA, provides an end-to-end security infrastructure suitable for multi-institution collaborations with support for grid computing, cloud computing, and web portals.
MyProxy
MyProxy is an online credential repository. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network.

Standards, Terminologies & Ontologies

BXH/XCEDE Tools
A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.
NeuroLex (formerly BIRNLEX)
NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.
XML-Based Clinical Experiment Data Exchange Schema (XCEDE)
Provides an extensive metadata hierarchy for describing and documenting research and clinical studies.

Collaboration Services

Capability Registry
Status: In testing (forecast for October 2009)
The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN [...]
Globus Clients
The Globus clients software provides MyProxy, GSI security, GridFTP, UberFTP, and RLS client software that enables users and applications to interact with BIRN operated MyProxy, GridFTP, and RLS servers.

	BIRN – Biomedical Informatics Research Network About About: Overview BIRN Video Introduction BIRN FAQs History News Executive Committee Steering Committee Presentations/Publications Media Sponsors Contact Us Capabilities Capabilities: Overview Current Capabilities Developing Capabilities Working with BIRN Working with BIRN: Overview FAQ BIRN User Inquiry Working Groups Data Management Working Group Genomics Working Group Information Integration Working Group Knowledge Engineering Working Group Operations Working Group Security Working Group Workflows Working Group Mailing Lists Resources Resources: Overview Tools Alphabetical List of 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 Share Your Tools Software License Best Practices Brain Morphometry Multi-site Studies Brain Morphometry Imaging Protocols Brain Morphometry MRI Phantom DTI Multisite Processing Functional MRI Multi-site Studies 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 Data Alphabetical List of Data Current Users Current Users: Overview Brain Morphometry BIRN Brain Morphometry BIRN Publications Cardiovascular Research Grid Function BIRN Function BIRN Publications Mouse BIRN Mouse BIRN Publications Nonhuman Primate Research Consortium Taub Institute for Research at Columbia University Tools This section includes a catalog of various tools made available through BIRN – these are tools developed and used in the BIRN community that others in the biomedical community may find helpful for their projects. These tools range from data sharing and user authentication tools to domain tools developed by the BIRN testbeds. Many of the following tools are made available through NITRC: We’ve listed tools by the following general categories (you can also see a strictly alphabetized list of tools): Acquisition, Calibration and Quality Assurance Data Upload, Storage and Management Data Sharing and Collaboration Image Database Access Analysis and Processing Visualization and Atlasing Security Standards, Terminologies & Ontologies Collaboration Services List of Tools by Category Acquisition, Calibration and Quality Assurance B0 and Eddy Current Correction Code for Diffusion MRI Software tool (executable plus code) and recommendations for acquisition protocols to correct distortions in diffusion MR images generated by main magnetic field inhomogeneities and eddy currents. DTI Gradient Table Creator DTI Gradient Table Creator computes the correct gradient table (i.e., the list of vectors that describe the diffusion weighting directions to use for analysis) for DTI acquisitions on Philips MRI scanners. EPrime Phase II These are E-prime programs for presenting stimuli to, collecting responses, and analyzing behavior from subjects. Eprime Programs from Function BIRN Phase I Traveling Subjects Employed during the FBIRN traveling subjects’ study of 2003, this is a Function-BIRN led study to standardize and calibrate imaging data for multi-site MRI studies by examining the brains of five subjects at nine different scanning sites across America. Function BIRN Stability Phantom QA Procedures Used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans. Gradient non-linearity distortion correction The goal of this software is to provide a 3D correction of image distortions in MRI data due to non-linearity of the magnetic fields from the imaging gradient coils. Data Upload, Storage and Management BXH/XCEDE Tools A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools. 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. Clinical Assessment Layout Manager (CALM) Helps incorporate online clinical assessment entry forms. GridFTP GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks. Human Imaging Database (HID) System Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities. NeuroLex (formerly BIRNLEX) NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction. XML-Based Clinical Experiment Data Exchange Schema (XCEDE) Provides an extensive metadata hierarchy for describing and documenting research and clinical studies. XNAT The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data. Data Sharing and Collaboration BIRN_ID Generator The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment. BXH/XCEDE Tools A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools. 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. Clinical Assessment Layout Manager (CALM) Helps incorporate online clinical assessment entry forms. Defacer for Structural MRI This algorithm, which is still under the validation phase, locates the subject’s facial features and removes them without disturbing brain tissue. Federated Informatics Research Environment (FIRE) FIRE (coming in 2010) is an integrated suite of tools to put your data on a gridFTP set of servers, link it to a database which is automatically federated, to be able to retrieve it from multiple sites, with the data wrapped in XCEDE (XML) wrappers. Human Imaging Database (HID) System Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities. NeuroLex (formerly BIRNLEX) NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction. XNAT The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data. Image Database Access Automated Image Registration (AIR) A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. BrainSuite BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head. LONI Debabler The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats. LONI Inspector The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files. LONI Provenance Editor The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information. LONI Visualization Tool (LOVE) An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. Mouse BIRN Atlasing Toolkit (MBAT) MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace. Registration using Embedded Maps (REM) REM registers N-D image pairs that may contain topological differences. Analysis and Processing BXH/XCEDE Tools A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools. CATNAP CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program) is an end-to-end data processing pipeline for Philips PAR/REC Magnetic Resonance data files. DTI Gradient Table Creator DTI Gradient Table Creator computes the correct gradient table (i.e., the list of vectors that describe the diffusion weighting directions to use for analysis) for DTI acquisitions on Philips MRI scanners. FBIRN Image Processing Scripts FIPS is a package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control. FreeSurfer Set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface. LONI Pipeline Provides a visual programming interface that allows researchers to link many independently developed analysis programs into a processing “pipeline.” XCEDE SPM Toolbox Captures the results from activation maps using the XCEDE schema. Visualization and Atlasing 3D Slicer Open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data. Automated Image Registration (AIR) A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. BrainSuite BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head. LONI Debabler The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats. LONI Inspector The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files. LONI Provenance Editor The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information. LONI Visualization Tool (LOVE) An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. Mouse BIRN Atlasing Toolkit (MBAT) MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace. MRI Studio MRI Studio is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration. Registration using Embedded Maps (REM) REM registers N-D image pairs that may contain topological differences. Security GAMA Grid Account Management Architecture, GAMA, provides an end-to-end security infrastructure suitable for multi-institution collaborations with support for grid computing, cloud computing, and web portals. MyProxy MyProxy is an online credential repository. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network. Standards, Terminologies & Ontologies BXH/XCEDE Tools A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools. NeuroLex (formerly BIRNLEX) NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction. XML-Based Clinical Experiment Data Exchange Schema (XCEDE) Provides an extensive metadata hierarchy for describing and documenting research and clinical studies. Collaboration Services Capability Registry Status: In testing (forecast for October 2009) The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN [...] Globus Clients The Globus clients software provides MyProxy, GSI security, GridFTP, UberFTP, and RLS client software that enables users and applications to interact with BIRN operated MyProxy, GridFTP, and RLS servers. Resources: Overview Tools Alphabetical List of Tools Federated Informatics Research Environment (FIRE) Primer fMRI Imaging Quality Assurance Methods fMRI Scanner Calibration Methods and Recommendations Functional Imaging Calibration Paradigms Multi-site Cognitive Paradigms for fMRI studies Share Your Tools Software License Best Practices Brain Morphometry Multi-site Studies Brain Morphometry Imaging Protocols Brain Morphometry MRI Phantom DTI Multisite Processing Functional MRI Multi-site Studies 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 Data Alphabetical List of Data BIRN Wiki BIRN Documentation Function BIRN Mouse BIRN Morph BIRN 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.