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ResourceDescriptionSupported PlatformsSupported Formats
3D Slicer
Neuroimaging Analysis Center
NIBIB

3D Slicer (Slicer) is a free, open source software package for image analysis and scientific visualization. Slicer is used in a variety of medical applications, including autism, multiple sclerosis, systemic lupus erythematosus, prostate cancer, schizophrenia, orthopedic biomechanics, COPD, cardiovascular disease and neurosurgery.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Annotations
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D Slicer and is used to create and edit annotations, use rulers to measure tumor diameters.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Change Tracker Wizard
Neuroimaging Analysis Center
NIBIB

ChangeTracker is a 3D Slicer module for quantification of the subtle changes in 3D images of pathology. It has been tuned specifically for

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer DICOM
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D Slicer that provides support for a subset of the DICOM standard including query/retrieve, store, and a local database.

Linux, Mac OSX, Windows DICOM
3D Slicer DTI Import/Export
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module imports and exports tensor datasets from various formats, including the NifTi file format.

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more)
3D Slicer DWI to DTI Estimation
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module performs a tensor model estimation from diffusion weighted images.

Linux, Mac OSX, Windows DICOM, MetaImage (.mha), MetaImage...(more)
3D Slicer Editor
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D slicer for manual segmentation of volumes. Some of the tools mimic a painting interface like photoshop or gimp, but work on 3D arrays of voxels rather than on 2D pixels.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer EM Segmentation with Atlas
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer module for atlas-based Expectation-Maximization segmentation of volume data.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer IGyne
National Resource Center for Image-Guided Therapy
NIBIB

This is a 3D Slicer extension module to support MR-Guided interstitial brachytherapy for gynecologic cancer.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Image Registration
Neuroimaging Analysis Center
NIBIB

This is an introduction to using the various image registration algorithms in 3D Slicer, and how to select the most suitable one.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Joint Rician LMMSE DWI Image Filter
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images

Linux, Windows DICOM, MetaImage (.mha), MetaImage...(more)
3D Slicer LongitudinalPETCT
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module that provides standardized uptake value (SUV) based on bodyweight for different regions of interest and for different timepoints.

Linux, Mac OSX, Windows DICOM, DICOM PET/CT
3D Slicer N4ITK Bias Field Correction
Neuroimaging Analysis Center
NIBIB

This is one of the many ITK filters provided in 3D Slicer. It performs MRI bias correction using N4 algorithm

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer OpenIGTLink Interface
National Resource Center for Image-Guided Therapy
NIBIB

The 3D Slicer OpenIGTLink Interface Module is a program module for network communication with external software/hardware using the OpenIGTLink protocol.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Region Growing Segmentation
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer module for region growing segmentation based on intensity statistics.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Resample Images
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer module for changing the resolution and spacing of an image.

Linux, Mac OSX, Web-Based Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Robust Statistics Segmentation
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module is a general purpose segmenter that evolves an contour model to extract the desired boundary of the object.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer TubeTK
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module that provides a toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer UKFTractography
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module for performing a particular style of diffusion image tractography that uses an unscented Kalman filter.

Linux, Mac OSX, Windows DICOM, MetaImage (.mha), MetaImage...(more)
3D Slicer Volume Rendering
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D Slicer and is used for interactive volume rendering of 3D image data.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer Volume Statistics
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module calculates image and volume properties using and label map and a grayscale image.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer VolumeResliceDriver
National Resource Center for Image-Guided Therapy
NIBIB

This is a 3D Slicer extension module to provide rapid reslicing of slices. The module is designed for image-guided therapy applications, where surgical tools are navigated by resliced volumetric image or real-time images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D Slicer XNATSlicer
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module that provides secure graphical-user interface based input/output exchange betwen 3D Slicer and any XNAT Server.

Windows Analyze (.hdr), Analyze (.img.gz),...(more)
3D SlicerRT
National Resource Center for Image-Guided Therapy
NIBIB

This is a 3D Slicer extension module that provides for radiotherapy.

Linux, Mac OSX, Windows DICOM, DICOM RT
ADAPT
Biomedical Simulations Resource (BMSR)
NIBIB

A computational modeling platform for pharmacokinetic /pharmacodynamic analysis and systems pharmacology. Contains high-level software tools for early- through late-phase drug development, as well as clinical pharmacology applications.

Windows
AlignTK
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

AlignTK is an image alignment toolkit. It is designed for batch-oriented alignment of a large number of 2-D images in either 2 or 3-dimensions.  Although it has been applied most extensively to electron-microscopy (EM) images of neural tissue, the package can be used with arbitrary grayscale images.  Multiple image formats are supported.

Linux
ANM
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

ANM (Anisotropic network model) is a simple tool for predicting the collective motions of molecular systems introduced using Elastic Network Models (ENM) and normal mode analysis. The biomolecular system is represented as a network, or graph, the nodes of which are the residues and the springs are their interactions. The model helps elucidate the intrinsic dynamics of proteins and their complexes and make inferences on functional mechanisms.

Web-Based
Appion
National Resource for Automated Molecular Microscopy
NIGMS

Appion is a "pipeline" for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.

Linux
APU
Center for Functional Imaging Technologies
NIBIB

APU (Atlas-guided Photon-migration Utilities) provides utilities for using a structural MRI (from an atlas or any other MRI) to guide the analysis of Near Infra-Red Spectroscopy (NIRS) data. These tools are used in conjunction with FreeSurfer and MNE.

Linux, Mac OSX, Windows AFNI, DICOM, GIFTI, MGZ,...(more)
Array Sensitivity Metric Software
Center for Functional Imaging Technologies
NIBIB

This reconstruction program runs on the Siemens scanner generating Dicom images of the array SNR computed with the Optimum method (uses noise correlation matix) and Sum of Squares (SoS).

BGE - Brain Graph Editor
Laboratory of Neuro Imaging Resource
NIBIB

The BrainGraph Editor is a JAVA based tool that allows researchers to create taxonomies or hierarchies to classify and organize information such as anatomy, connectivity, and developmental stages.

Linux, Mac OSX, Windows
BiblioSpec
Yeast Resource Center
NIGMS

A suite of software tools for creating and searching MS/MS peptide spectrum libraries. The software is particularly useful for those performing repeated proteomics profiling experiments on the same organism. After the identity of a peptide spectrum has been determined, this information can be used to speed and improve all future analyses.

Linux, Windows
BioMesh3D
Center for Integrative Biomedical Computing (CIBC)
NIGMS

A tetrahedral mesh generator, capable of generating multi-material quality meshes out of segmented biomedical image data. Integrated with SCIRun to visualize the intermediate results.

Linux, Mac OSX, Windows NRRD (.nhdr), NRRD (.nrrd)
BioNetGen
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks.

Linux, Mac OSX, Windows
Brain
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program identifies the largest contiguous solid within a T2 image.

Windows HDF
BreastPro
Center for Magnetic Resonance and Optical Imaging
NIBIB

This package includes a 3D simultaneous bilateral back-projection sequence for dynamic contrast-enhanced imaging of the breasts. Data from both breasts are acquired simultaneously using a 3D hybrid sequence in which data are acquired radially in-plane and the slices are phase-encoded. The signal from each breast is saved separately and residual slice aliasing from one volume into the other is removed using SENSE reconstruction. An effective temporal resolution of 15 seconds for both breast volumes is...

Linux, Mac OSX, Windows
Bullseye
Yeast Resource Center
NIGMS

Bullseye takes high resolution accurate masses from full scan spectra and matches these masses to tandem MS scan events. The MS/MS spectra can then be database searched with a narrow precursor ion mass to reduce database search space and improve peptide sequence identification.

Linux
CA Portal: The Computational Anatomy Portal
Resource for Quantitative Functional MRI
NIBIB

For analyzing and interpreting anatomical images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
CBio Portal
National Resource for Network Biology
NIGMS

cBio Cancer Genomics Portal provides visualization, analysis and download of large-scale cancer genomics data sets. With NRNB funding, the portal now enables researchers to dynamically visualize, analyze and filter cancer genomic data in the context of pathways and interaction networks derived from Pathway Commons. Network visualization is provided by cytoscape.js.

Web-Based BioPAX
CellBlender
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

CellBlender is a Blender addon for creation, simulation, visualization, and analysis of realistic 3D Cell Models. CellBlender leverages the full-featured 3D content creation capabilities of Blender to support a rich environment for the creation of simulation-ready, biophysically realistic models of the microscopic structure and biochemical function of cells.

CellBlender is fully functional with MCell and partially functional with SBML (http://sbml.org). We invite the computational cell biology community to contribute to the project, adding features and support...

Linux, Mac OSX, Windows
CellOrganizer
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

The CellOrganizer project provides tools for

  • learning generative models of cell organization directly from images
  • storing and retrieving those models in XML files
  • synthesizing cell images (or other representations) from one or more models

Model learning captures variation among cells in a collection of images. Images used for model learning and instances synthesized from models can be two- or three-dimensional static images or movies.

Linux, Mac OSX
Census
Yeast Resource Center
NIGMS

Quantitative Analysis Tool for both labeling and labeling free analysis. Visit Census web page for more info.

Linux, Mac OSX, Windows
CEST Z-spectral simulations
Resource for Quantitative Functional MRI
NIBIB

Uses Bloch equations to simulate Z-spectra for 2-pool system

Web-Based
CFMBIS - Charged Fluid Model for Brain Image Segmentation
Laboratory of Neuro Imaging Resource
NIBIB

CFMBIS is a computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data.

Linux, Unix, Windows
CGoct3D
Resource for MRI of Neurodegenerative Disorders
NIBIB

CGoct3D is a program to perform K-Bayes optimization of multi-slice ASL-perfusion datasets.

Binary
Charge Prediction Machine (CPM)
Yeast Resource Center
NIGMS

Charge Prediction Machine: Tool for Inferring Precursor Charge States of Low Resolution.

chemViz2
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A plugin to Cytoscape that links network visualization in Cytoscape with cheminformatics, namely 2D display of small molecules and calculation of chemical descriptors and Tanimoto similarities.

Chimera (UCSF Chimera)
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A package for the interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, conformational ensembles, and trajectories.

Linux, Mac OSX, Windows Aligned FASTA, Aligned NBRF/PIR,...(more)
CIS Software
Resource for Quantitative Functional MRI
NIBIB

For analyzing and interpreting anatomical images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
Cluster probability
NMR Imaging and Localized Spectroscopy
NIBIB

This program is a direct implementation of the following paper: Jinhu Xiong, et al. "Clustered Pixels Analysis for Functional MRI Activation Studies of the Human Brain" Human Brain Mapping, 3:287-301(1995).

Unix
clusterMaker2
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A plugin to Cytoscape that provides several clustering methods and links between different displays of the results such as node hierarchies and heat maps.

Crux
Yeast Resource Center
NIGMS

Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra.

Linux FASTA, MS2, SQT, Text...(more)
CSX3
Resource for Quantitative Functional MRI
NIBIB

MRS and MRSI Analysis. csx3 is free software available for download that processes and displays MR spectroscopic and spectroscopic imaging (MRSI) datasets. It is particularly designed for the quantitative analysis and visualization of MRSI data.

Linux, Mac OSX, Unix DICOM, GE, Philips, Siemens,...(more)
Cylinder
Center for Magnetic Resonance and Optical Imaging
NIBIB

CYLINDER is a GUI driven program that uses MRI to quantitatively determine recording electrode trajectories and their intersection with desired brain anatomy. This program can be used to guide electrode placement specific to the anatomy of an individual subject.

Cytoscape
National Resource for Network Biology
NIGMS

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of experiment data and annotation. A large and growing collection of apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Linux, Mac OSX, Windows BioPAX, GML, JSON, SBML,...(more)
cytoscape.js
National Resource for Network Biology
NIGMS

Cytoscape.js is a reusable component that allows you to embed networks within HTML documents. It is easily integrated in HTML via its Javascript API and customisable in what data it loads and how it visually displays that data. It is an open source bioinformatics environment for integration, visualization, and query of biological networks that can be used with a broad variety of data types and customized through the use and development of plugin extensions.

Web-Based JSON
DanteR
Proteomics Research Resource for Integrative Biology
NIGMS

Used to perform various downstream data analysis, data reduction, and data comparison steps including normalization, hypothesis testing and clustering.

Linux, Mac OSX, Windows Excel, Text (.txt)
Dcm2gen
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

This software converts from DICOM to GE Genesis 5.x image file format (MR images only).

Decon2LS
Proteomics Research Resource for Integrative Biology
NIGMS

Used to de-isotope MS spectra and to detect features from MS data using isotopic signatures of expected components.

Windows Agilent Wiff, Bruker, Micromass,...(more)
DeconMSn
Proteomics Research Resource for Integrative Biology
NIGMS

Used to create .Dta files or .MGF files from tandem MS/MS data (Thermo Finnigan or mzXML format) with accurate parent monoisotopic mass and charge determined using the isotopic signatures of the parent ions.

Windows mzXML, Thermo Raw
DFCalc
Yeast Resource Center
NIGMS

Biological mass spectrometry need not be limited to peptides, of course. DFCalc is software designed to assist the interpretation of tandem mass spectra from DNA molecules. The program predicts the fragment ions for known sequences, producing a list to be compared against a spectrum.

DicomToHdf
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program converts Dicom data to HDF version 4.2 format. The windows command-line version of the dicom2 program is used to translate the Dicom header. Dicom files from the parent directory are cataloged and combined into a single HD volume when possible.

Windows DICOM
DiD - LONI De-identification Debablet
Laboratory of Neuro Imaging Resource
NIBIB

A simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files. Removal of this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.

Linux, Mac OSX, Windows
Diffusion Tensor Image Post-Processing
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

Post-processing routines for reconstruction of diffusion tensor images. Precompiled binaries for Unix/Linux are available. Please send email to Mike Moseley (mike@lucas.stanford.edu) stating your name and research institute. Instructions for downloading this software package will be sent to you. For more details, visit http://rsl.stanford.edu/moseley/tensorcalc

DIRAC - Diffusion Imaging Reconstruction and Analysis Collection
Laboratory of Neuro Imaging Resource
NIBIB

DIRAC is a collection of tools for rapid and robust processing of diffusion-weighted imaging (DWI) data. Programs are included for both diffusion tensor and HARDI reconstruction and analysis.

Linux, Mac OSX, Windows
DPS - LONI Distributed Pipeline Server Installation Utility
Laboratory of Neuro Imaging Resource
NIBIB

DPS is a utility that streamlines the process of setting up an independent Pipeline environment. The interface walks a user through several steps, providing default preferences along the way, but also gives the user flexibility in configuring the resulting system. As a result, this tool is designed to be used by neuroscientists, bioinformaticians, and system administrators alike.

Linux
DSM - DualSurfaceMin
Laboratory of Neuro Imaging Resource
NIBIB

The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images.

Linux, Unix Analyze (.hdr), Analyze (.img.gz),...(more)
DtaRefinery
Proteomics Research Resource for Integrative Biology
NIGMS

Improves mass measurement errors for parent ions of tandem MS/MS data by modeling systematic errors based on putative peptide identifications. This information is used to subtract out errors from parent ion protonated masses.

Windows Concatenated DTA.txt, DTA
DTASelect/Contrast
Yeast Resource Center
NIGMS

DTASelect and Contrast were designed to make interpretation and comparison of proteomic data faster and more effective. DTASelect organizes and filters SEQUEST identifications, reducing the time required to interpret the results for each sample. Contrast differentiates multiple samples and comprises a powerful meta-analytical tool.

Linux, Mac OSX, Windows MS2, SQT
EMAN2
National Center for Macromolecular Imaging
NIGMS

Full featured scientific image processing suite. Mainly targeted at the transmission electron microscopy community, but also used in other areas. Includes a library of nearly 1000 algorithms with an integrated openGL GUI and full Python bindings.

Linux, Mac OSX, Windows Amira, CNS or XPLOR...(more)
EMEN2
National Center for Macromolecular Imaging
NIGMS

Electronic lab notebook and  Object oriented database (OODB). Flexible web-based interface requires no database experience to use, yet permits rich data mining/query capabilities. Currently supports 600+ users with >15 TB of image data, yet trivial to install for small-scale sites. Python based.

Linux, Mac OSX AJAX, Binary
EONS
Biomedical Simulations Resource (BMSR)
NIBIB

The EONS (Elementary Objects of the Nervous System) software allows in-depth study of a number of synaptic components (presynaptic terminal, postsynaptic spine and astrocytic ensheathment), as well as their complex spatial and temporal interactions.

Linux, Mac OSX, Windows
Extractor
Center for Magnetic Resonance and Optical Imaging
NIBIB

EXTRACTOR is a graphical user interface written in the IDL. The program is a tool for the extraction and segmentation of sub-volumes from a 3D image data set. The program permits the interactive selection of standard image processing operations, including pixel intensity threshholding, seed growing, boundary tracing, and morphological dilation and erosion.

Analyze (.hdr), Analyze (.img.gz),...(more)
Fast Imaging Library Toolkit
National Resource Center for Image-Guided Therapy
NIBIB

A library of functions which provides a number of algorithms to reconstruct accelerated MR data, including UNFOLD, Parallel Imaging Methods, Homodyne processing of partial-Fourier data, Gradient field inhomogeneity correction (gradwarp) and Nyquist Ghost correction.

EPI data by Brigham...(more)
FASTMAP
NMR Imaging and Localized Spectroscopy
NIBIB

FASTMAP is a shimming technique based on measuring B0 field plots along projections instead of mapping whole imaging planes with the benefit of improved speed and performance.

Varian FID
FFT Library
Laboratory of Neuro Imaging Resource
NIBIB

The FFT library is used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms

Linux, Mac OSX, Windows
FluoRender
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Interactive rendering tool for confocal microscopy data visualization. Designed for neurobiologists, to help them better visualize fluorescent-stained confocal samples.

Windows Confocal Data
FourPhasePerf
Resource for MRI of Neurodegenerative Disorders
NIBIB

The FourPhasePerf program is a Matlab program designed to obtain quantitative measures of cerebral blood flow from arterial spin labeling (ASL) MRI data.  It calculates hemodynamic parameters based on a four phase ASL model.  In this dual-compartment distributed perfusion model, the bolus arrival time is decomposed into transit delays through large arteries and delays through smaller arteries and arterioles, expressed as arterial-arteriole transit time (aaTT), before the spin labels reach the capillary bed and perfusion...

Linux, Mac OSX, Windows ASL values of a...(more)
Freesurfer & FS-Fast
Center for Functional Imaging Technologies
NIBIB

The FreeSurfer package is a suite of tools for segmentation, registration, surface reconstruction and processing of general neuroanatomical models of the human brain. It includes FS-Fast fMRI data analysis tools. (Freesurfer Wiki)

Linux, Mac OSX, Windows AFNI, DICOM, GIFTI, MGZ,...(more)
FRETSCAL
Yeast Resource Center
NIGMS

FRETSCAL screens images of cells that contain CFP and YFP tagged proteins in order to determine the extent of energy transfer (FRET) between the two fluorophores. The graphical user interface (GUI) of FRETSCAL allows the user to specify criteria that are used to identify areas of interest (AOIs) in the images.

Matlab
GAMIXTURE Matlab toolbox
Laboratory of Neuro Imaging Resource
NIBIB

GAMIXTURE is a collection of software for solving complex finite mixture model parameter estimation problems in neuroimaging. At the moment, the Matlab package for the FMM parameter estimation is available.

Linux, Mac OSX, Windows Matlab
Gannet
Resource for Quantitative Functional MRI
NIBIB

GABA-Edited MRS Analysis Gannet is free software available for download that processes and displays GABA-edited MRS datasets. It is designed for the quantitative batch-analysis and visualization of GABA-edited data with minimal user intervention.

GE, Philips, Siemens, spectroscopy...(more)
Gehdr2matlab
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

Convert rdbm.h and imagedb.h into a Matlab script for reading/writing GE raw data headers.

GlycomicsPortal
National Center for Biomedical Glycomics (NCBG)
NIGMS

GlycomicsPortal is a web based registry for glyco-bioinformatics tools (e.g. software, databases, ontologies, web services, workflows).

Web-Based
GTKDynamo
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods. Pymol has been chosen as a graphical interface to pDynamo because it has a python API with wide documentation available.

Linux, Mac OSX
GutenTag
Yeast Resource Center
NIGMS

GutenTag is software to identify peptides by the sequence tagging technique. SEQUEST searches a sequence database by mass, but GutenTag searches with short sequences derived directly from the spectrum.

Hardklor
Yeast Resource Center
NIGMS

A computer program for the analysis of high resolution mass spectrometry data. Hardklor will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions.

HF-1
Center for Functional Imaging Technologies
NIBIB

An Open-Source Hardware and Software Platform for Simultaneous Electrophysiology and MRI

Windows ascii, Binary, RAW
HomER
Center for Functional Imaging Technologies
NIBIB

HomER (Hemodynamic Evoked Response) graphical interface for visualization and analysis of Near Infra-Red Spectroscopy (NIRS) data.

Linux, Mac OSX, Windows
ICR-2LS
Proteomics Research Resource for Integrative Biology
NIGMS

Finds peaks in raw mass spectra. Capable of full waveform generation, automated mass spectra interpretation and databas searching integration of FASTA or GenBank files.

Windows Agilent Wiff, Bruker, Micromass,...(more)
IDCalc
Yeast Resource Center
NIGMS

An implementation of the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions.

Windows
iGNM
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and...

Web-Based
ImageVis3D
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Highly scalable volume rendering program.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
IMAX3
Resource for Quantitative Functional MRI
NIBIB

MRS and MRSI Analysis. csx3 is free software available for download that processes and displays MR spectroscopic and spectroscopic imaging (MRSI) datasets. It is particularly designed for the quantitative analysis and visualization of MRSI data.

Linux, Mac OSX, Unix DICOM, GE, Philips, Siemens,...(more)
Import
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program converts Siemens VISION system MR images (ACR-NEMA) to HDF format.

Windows ACR-NEMA
Imscribe
Center for Magnetic Resonance and Optical Imaging
NIBIB

ImScribe is a Matlab program designed to automate the specification of the acquisition Field-of-View with Siemens MRI scanners. The program is particularly suited for neuro-imaging, including fMRI.

DICOM, GE, Philips, Siemens,...(more)
iso2mesh
Center for Functional Imaging Technologies
NIBIB

iso2mesh is a free matlab/octave-based mesh generation and processing toolbox. It can create 3D tetrahedral finite element (FE) mesh from surfaces, 3D binary and gray-scale volumetric images such as segmented MRI/CT scans.

Linux, Mac OSX, Windows ABAQUS, ASC, COMSOL, DXF,...(more)
jViewbox
Laboratory of Neuro Imaging Resource
NIBIB

A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple and yet extensive API that provides the core functionality of 2-D image presentation needed by most imaging applications.

Irix, Linux, Mac OSX, Unix, Windows
LDDMM Suite
Resource for Quantitative Functional MRI
NIBIB

For analyzing and interpreting anatomical images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
Leginon
National Resource for Automated Molecular Microscopy
NIGMS

Leginon is a system designed for automated collection of images from a transmission electron microscope.

Linux
LONI Brain Parser
Laboratory of Neuro Imaging Resource
NIBIB

Brain Parser software segments regions of interest based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Windows
LONI Debabeler
Laboratory of Neuro Imaging Resource
NIBIB

The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats. Its visual programming environment provides an intuitive and easy way to modify a variety of existing translations to meet researcher's needs.

Irix, Linux, Mac OSX, Unix, Windows
LONI ICE - It's Close Enuf
Laboratory of Neuro Imaging Resource
NIBIB

LONI ICE is a Java application that generates seed points for other image processing applications. ICE stands for "It's Close Enuf" and implies that the seed points it generates are "close enough" to be useful.

Linux, Mac OSX, Windows
LONI Inspector
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Mac OSX, Windows AFNI, Analyze (.hdr), Analyze...(more)
LONI Java Image I/O Plugins
Laboratory of Neuro Imaging Resource
NIBIB

Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.

Linux, Mac OSX, Windows AFNI, Analyze (.hdr), Analyze...(more)
Lorikeet
Yeast Resource Center
NIGMS

Lorikeet is a JQuery plugin to view MS/MS spectra annotated with fragment ions. The viewer is interactive with zoom capabilities, selection of fragment types, switching annotations on and off etc. The plugin can, optionally, also render a MS1 spectrum below the MS/MS spectrum. Lorikeet uses the Flot plotting library.

Web-Based
LOVE
Laboratory of Neuro Imaging Resource
NIBIB

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.

Linux, Unix, Windows
Lxgrab
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

Take a snapshot of a GE console screen. Download PERL script.

LYSIS
Biomedical Simulations Resource (BMSR)
NIBIB

LYSIS is an interactive set of modular programs that provide an integrated computing environment for data analysis and system modeling, emphasizing input-output nonlinear system modeling and the novel methodology of

Linux, Mac OSX, Windows Matlab
MakeMS2
Yeast Resource Center
NIGMS

A windows client program used to produce compact and easily parsed text based file formats for shotgun proteomic spectra and indentifications.

Windows
map3d
Center for Integrative Biomedical Computing (CIBC)
NIGMS

A scientific visualization application to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models.

Linux, Mac OSX, Windows ascii, Binary, Matlab
MASIC
Proteomics Research Resource for Integrative Biology
NIGMS

Generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis.

Windows mzXML, Thermo Raw
MAST - Morphometric Atlasing Statistical Toolkit
Laboratory of Neuro Imaging Resource
NIBIB

The Morphometric Atlasing Statistical Toolkit is a collection of tools which deals with the general problem of creating statistical maps of data from populations of subjects.

Linux, Mac OSX, Windows CCBBM, Duff, MINC, Minc...(more)
MatCoil
Resource for MRI of Neurodegenerative Disorders
NIBIB

MATCOIL is a program written in Matlab with GUI interfaces that enables both single surface coils and surface coil configurations to be designed, and the resulting B1 fields and sensitivity fields to be calculated and displayed. Additional parameters, such as tip angle, and vector field plots of the B1 field, are also available. The coil shapes may be varied from circular, to elliptical, to rectangular, and may be planar or wrapped about a circular cylinder.  In addition,...

Linux, Mac OSX, Windows Matlab
MatMRI
Resource for MRI of Neurodegenerative Disorders
NIBIB

The MATMRI program is written in Matlab and calculates magnetization transfer (MT) effects in MP RAGE experiments based saturation of the bound pool as calculated and discussed by Henkelmann et al. (Magn Reson Med 19997; 37, 866) and on the formulations for transfer of MT provided by Helms and Hagberg (Concepts Magn Reson 2004; 21, 37).  The program is presently being re-written, and some features may not work.  Contact Dr. Matson for details.

Linux, Mac OSX, Windows Matlab
MatPulse
Resource for MRI of Neurodegenerative Disorders
NIBIB

MATPULSE is a program written in Matlab with GUI interfaces that enables calculation of Shinnar-LeRoux (SLR) frequency selective RF pulses. The program also provides pulse re-mapping (the MATPULSE version of VERSE), and includes a Bloch equations section, and a variety of other calculations, including gradient refocusing, and calculation of the effects due to relaxation. Additional features include pulse concatenation, root reflection, calculation of the effects  of flow, and optimization of pulses with immunity to B1...

Linux, Mac OSX, Windows Matlab
MBAT - Mouse BIRN Atlasing Toolkit
Laboratory of Neuro Imaging Resource
NIBIB

MBAT provides a workflow environment bringing together online resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. MBAT is written in java so it is platform independent and is extensible through its plugin architecture.

Linux, Mac OSX, Windows
MCell
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

MCell is a Monte Carlo reaction-diffusion simulator for modeling computational microphysiology in arbitrarily complex 3D spatial geometries.

As a modeling tool, MCell creates realistic simulations of cellular signaling in the complex 3fD subcellular microenvironment in and around living cells -- what we call cellular microphysiology. At such small subcellular scales the familiar macroscopic concept of concentration is not useful and stochastic behavior dominates. MCell uses highly optimized Monte Carlo algorithms to track the stochastic behavior of...

Linux, Mac OSX, Windows
MCX
Center for Functional Imaging Technologies
NIBIB

Monte Carlo eXtreme (MCX) is Monte-Carlo simulation software for modeling photon migration in 3D turbid media. Using GPU-based massively parallel computing techniques, it is hundreds times faster compared to traditional CPU-based simulation.

Linux, Mac OSX, Windows JSON
MLS - Model-based Level Set
Laboratory of Neuro Imaging Resource
NIBIB

MLS is an algorithm and application for skull-stripping magnetic resonance.

MRI
MMC
Center for Functional Imaging Technologies
NIBIB

Mesh-based Monte Carlo, or MMC, is a Monte Carlo (MC) solver for photon migration in 3D turbid media. MMC can represent a complex domain using a volumetric mesh, thus giving better accuracy and computational speed.

Linux, Mac OSX, Windows JSON
MNE
Center for Functional Imaging Technologies
NIBIB

Software for anatomically and functionally constrained MEG/EEG source modeling. Includes tools for preprocessing, forward and inverse modeling, time-frequency analysis, connectivity, and statistics. MNE-C (compiled), MNE-Matlab and MNE-Python (toolboxes)

Linux, Mac OSX, Windows EEG, fif, MEG
Molecular Weight Calculator
Proteomics Research Resource for Integrative Biology
NIGMS

Calculates the molecular weight and percent composition of chemical formulas and amino acids.

Windows
Mouse brain segmentation pipeline
Integrated Center for In Vivo Microscopy
NIBIB

Suite of segmentation tools (Avants et al. 2008) for human neuroimaging adapted and streamlined for segmentation of mouse brain images acquired with multispectral MR protocols.

Mac OSX NifTI (.nia), NifTI (.nii,...(more)
MRFSEG+GAMIXTURE Software Bundle
Laboratory of Neuro Imaging Resource
NIBIB

MRFSEG+GAMIXTURE is a collection of tools implementing a flexible voxel classification framework. The framework is based on a novel genetic algorithm based finite mixture model (GAMIXTURE) and a standard 3-D Markov random field (MRF) based on the iterative conditional modes (ICM) algorithm (MRFSEG).

Linux
MriStudio
Resource for Quantitative Functional MRI
NIBIB

Inter-Subject MRI Co-Registration, DTI Processing, ROI Analysis to process large multimodal datasets between subjects by coregistering them to an atlas. MriStudio consists of DtiStudio, DiffeoMap, and RoiEditor. DtiStudio processes DTI data for tensor calculation and fiber tractography. DiffeoMap performs image transformation. RoiEditor applies atlas templates for automated image segmentation based on the results of DiffeoMap.

Windows Analyze (.hdr), Analyze (.img.gz),...(more)
MS File Info Scanner
Proteomics Research Resource for Integrative Biology
NIGMS

Scans a series of MS data files (or data folders) and extracts the acquisition start and end times, number of spectra, and the total size of the data, saving the values in the file DatasetTimeFile.txt.

Windows Agilent .D, Agilent Wiff,...(more)
MScout
Yeast Resource Center
NIGMS

MScout is a program that we have used for assessing LC-MS data quality.

Linux
MTM
NMR Imaging and Localized Spectroscopy
NIBIB

Multi-Taper Methods for signal/noise analysis described in P. Mitra and B. Pesaran,
"Analysis of Dynamic Brain Imaging Data" Biophys.J.1999 76:691-708

Varian FID
Multi-band EPI
NMR Imaging and Localized Spectroscopy
NIBIB

Highly-accelerated 2D EPI pulse sequence for Siemens scanners.  Sequences developed at CMRR are available for use at other institutions on compatible Siemens scanners by C2P agreement with CMRR and Siemens.

Linux Siemens VD11Ds
MultiAlign
Proteomics Research Resource for Integrative Biology
NIGMS

Aligns multiple LC-MS datasets to one another, afterwhich LC-MS features can be matched to a database of peptides (e.g. an AMT tag database).

Windows Decon2LS .CSV files, ICR2LS...(more)
MultiPhase-SEG
Laboratory of Neuro Imaging Resource
NIBIB

MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model.

Linux, Mac OSX, Windows
Mzxml2msn
Yeast Resource Center
NIGMS

Mzxml2msn is a Java program we developed to convert mzXML to ms1 and ms2 files. Although our ProLuCID and Census can handle mzXML files, we prefer to use ms2 and ms1 files for computational effeciency.

Linux, Mac OSX, Windows
NAMD
Center for Macromolecular Modeling and Bioinformatics
NIGMS

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations.

Linux, Mac OSX, Windows AMBER, AMBER 'binpos' trajectory...(more)
NBtoolbox
Surface Analysis Facility for Biomedical Problems
NIBIB

The NBToolbox is a free set of Matlab graphical user interfaces (GUIs) for multivariate analysis of ToF-SIMS spectra and images.

BIF3D, BIF6, Iontof BIF,...(more)
Neuroimaging Provenance XSD
Laboratory of Neuro Imaging Resource
NIBIB

The LONI Neuroimaging Provenance XSD is an XML schema Document for validating and describing .prov data provenance description files

Analyze (.hdr), Analyze (.img.gz),...(more)
NMR Kitchen
NMR Imaging and Localized Spectroscopy
NIBIB

NMRKITCHEN is a user-friendly program for simulating spin-system evolution during pulse sequences.

Windows
Nodupe
Yeast Resource Center
NIGMS

NoDupe identifies similarity among uninterpreted tandem mass spectra. Optionally, the program can remove duplicate copies of spectra.

Normalized Elution Time Prediction Utility
Proteomics Research Resource for Integrative Biology
NIGMS

Used to compute the predicted normalized elution time (NET) value for a list of peptide sequences.

Windows Text (.txt)
O2 Analysis - Analysis Software for 3He MRI
Center for Magnetic Resonance and Optical Imaging
NIBIB

This software calculates regional VA/Q ratios from the regional measurements of PAO2 by a variation on methods used to calculate PAO2 from a known VA/Q ratio.

DICOM, TIFF (.tiff, .tif,...(more)
OntologyWebApi
National Center for Biomedical Glycomics (NCBG)
NIGMS

The OntologyWebApi is a set of web services allowing programmatic access to knowledge stored in NCBG ontologies (e.g. GlycO, ReferO)

Web-Based
OpenIGTLink
National Resource Center for Image-Guided Therapy
NIBIB

OpenIGTLink provides a standardized mechanism for communication among computers and devices in operating rooms for wide variety of image-guided therapy (IGT) applications

OPTseq2
Center for Functional Imaging Technologies
NIBIB

optseq2 is a tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events)

Linux, Mac OSX, Windows AFNI, DICOM, GIFTI, MGZ,...(more)
PAnDA
Yeast Resource Center
NIGMS

An acronym for Post Analysis Data Acquisition. PAnDA uses the Hardklor feature finder to define the molecular species in an LC-MS analysis and then uses this information to automatically construct new methods to specifically target features that were missed in subsequent analyses. PAnDA is particularly powerful when running technical and biological replicates to increase the fraction of the features that can be assigned a peptide identity.

Parallel HDICA
Resource for Quantitative Functional MRI
NIBIB

High dimensional ICA analysis. Implements ICA for large dimensional data sets using Sun Grid Engine.

NifTI (.nia), NifTI (.nii,...(more)
PatternLab
Yeast Resource Center
NIGMS

Provides tools for analyzing shotgun proteomic data quantitated by spectral counting (with DTASelect) or labeling (with Census). The modules provide means to point differentialy expressed proteins / peptides (ACFold / TFold modules), find proteins with simmilar expression profiles in time-course experiments (TrendQuest module), find unique proteins to a state (Area proportional venn diagram module) and help interpreting results according to the Gene Ontology (Gene Ontology Explorer module). Minimum requirements: a computer with Windows XP SP2.

Windows
Peptide Hit Results Processor
Proteomics Research Resource for Integrative Biology
NIGMS

Converts an X!Tandem results file (XML format) or a SEQUEST Synopsis/First Hits file to a series of tab-delimited text files summarizing the results.

Windows Text (.txt), X!Tandem XML
Percolator
Yeast Resource Center
NIGMS

A semi-supervised machine learning approach for improving the analysis of tandem mass spectrometry data of peptides. Percolator uses a machine learning technique call a support vector machine to dynamically discriminate between correct and decoy spectrum identifications obtained by database searching. By using our approach, we are able to identify approximately 50% more peptides from a given µLC-MS/MS dataset.

Linux, Windows
Phase Map Cross-correlation Detection and Quantification (PDQ)
A Multidisciplinary NMR Center for Biomedical Research
NIBIB

A postprocessing algorithm with the purpose of automating identification and quantification of localized accumulations of SPIO agents.

Matlab
Phase Slope Magnitude (PSM) Image Analysis
A Multidisciplinary NMR Center for Biomedical Research
NIBIB

A postprocessing method which yields enhanced positive-contrast images from the phase map associated with T2* weighted MRI data.

Matlab
Philius
Yeast Resource Center
NIGMS

Philius uses Hidden Markov Models (HMM) to predict transmembrane protein topology and signal peptide position.

Linux
PhysioFix for Matlab
NMR Imaging and Localized Spectroscopy
NIBIB

PhysioFix is an implementation of the following paper for single-shot EPI fMRI: X. Hu, T. H. Le, T. Parrish and P. Erhard “Retrospective Estimation and Correction of Physiological Fluctuation in fMRI”  Magn. Reson. Med., 34:201-212 (1995)

Linux, Mac OSX, Windows Matlab, Varian FID
PhysioFix User's Guide
NMR Imaging and Localized Spectroscopy
NIBIB

PhysioFix is an implementation of the following paper for single-shot EPI fMRI: X. Hu, T. H. Le, T. Parrish and P. Erhard “Retrospective Estimation and Correction of Physiological Fluctuation in fMRI”  Magn. Reson. Med., 34:201-212(1995)

Linux, Mac OSX, Windows Matlab, Varian FID
Pipeline - LONI Pipeline Processing Environment
Laboratory of Neuro Imaging Resource
NIBIB

The LONI Pipeline is a free workflow application primarily aimed at Neuroimaging Researchers. With the LONI Pipeline, users can create workflows that take advantage of all the greatest Neuroimaging tools available, quickly.

PMI Toolbox
Center for Functional Imaging Technologies
NIBIB

Photon Migration Imaging (PMI) Toolbox for solving diffuse optical imaging (DOI) forward and inverse problems.

Linux, Mac OSX, Windows Matlab
PNEUMA
Biomedical Simulations Resource (BMSR)
NIBIB

PNEUMA consists of a set of Simulink modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions.

Linux, Mac OSX, Windows Matlab
Poisson Disk Distributrion for Sparse Sampling in MRI
Resource for MRI of Neurodegenerative Disorders
NIBIB

The program p_disk_dist.m is a Matlab program for calculation of a Poisson disk distribution on a Cartesian frame. The program includes a Matlab GUI interface for ease of use. A Poisson Disk distribution is superior to a random distribution for use as a sparse sampling pattern for MRI. The program supports a variety of options for tailoring the distribution to the desired pattern density.

Linux, Mac OSX, Windows Matlab
ProDy
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

ProDy is a free and open-source Python package for protein structural dynamics and sequence evolution analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development. NMWiz, a VMD plugin GUI, also accompanies ProDy for streamlining protein dynamics analysis calculations and enabling comparative visual analysis of experimental and theoretical data.
With ProDy, you can perform principal component analysis of heterogeneous X-ray structures, NMR models, and MD snapshots. Protein dynamics...

Linux, Mac OSX, Windows
ProLuCID
Yeast Resource Center
NIGMS

ProLuCID is a fast and sensitive tandem mass spectra-based protein identification program recently developed in the Yates laboratory at The Scripps Research Institute.

ProSightLite
National Resource for Translational and Developmental Proteomics
NIGMS

ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations.

Windows
Protein Digestion Simulator
Proteomics Research Resource for Integrative Biology
NIGMS

Used to read a text file containing protein or peptide sequences (Fasta format or delimited text) and output the data to a tab-delimited file.

Windows FASTA, Text (.txt)
Provenance Editor
Laboratory of Neuro Imaging Resource
NIBIB

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.

Analyze (.hdr), Analyze (.img.gz),...(more)
PWS - LONI Pipeline Web Start
Laboratory of Neuro Imaging Resource
NIBIB

The LONI Pipeline Web Start (PWS) has all of the features and functionality of the stand-alone Pipeline software application. Users can run PWS directly from their web browser. There is no need to register, download or install anything. You have immediate and direct access to the LONI Pipeline servers. As soon as you allow the program to launch, your workflow will start.

Web-Based
QCorr
Yeast Resource Center
NIGMS

The QCorr algorithm compares a tandem mass spectrum to a reversed copy of the same spectrum using a cross correlation.

Qrator
National Center for Biomedical Glycomics (NCBG)
NIGMS

Qrator is a web based application for the human curation of carbohydrate structures (glycans).

Web-Based
qvality
Yeast Resource Center
NIGMS

qvality performs nonparametric estimation of posterior error probabilities.

RawExtractor
Yeast Resource Center
NIGMS

RawExtractor is a program to extract MS and MS/MS spectra from RAW files generated by Thermo mass spectrometers, such as LTQ, LTQ-Orbitrap, LCQ, and stores the spectra in ms1, ms2 or mzXML file format. The spectra files generated by RawExtractor program are used as input for protein identification programs SEQUEST, ProLuCID and quantitatation program Census.

RelEx
Yeast Resource Center
NIGMS

Quantitative Analysis Tool. Visit RelEx web page for more info.

RELMODEL
NMR Imaging and Localized Spectroscopy
NIBIB

RELMODEL is a user- friendly program for calculation the relaxation parameters T1, T2 and correlation and spectral density functions from the molecular motion correlation times and restriction parameters.

Windows
REM - Registration using Embedded Maps
Laboratory of Neuro Imaging Resource
NIBIB

REM registers N-D image pairs that may contain topological differences. It produces an output reconstructed image and both a geometric and intensity transformation as a N-D vector field.

Linux, Mac OSX, Windows
Results
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program supports a broad range of processing, including logical operations, rigid body transformations, etc.

Windows HDF
RF Pulse Design
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

A library of Matlab routines developed by John Pauly (pauly@mrsrl.stanford.edu) for designing RF pulses using the Shinnar-Le Roux algorithm. Reference: Pauly J, Le Roux P, Nishimra D, Macovski A. Parameter relations for the Shinnar-Le Roux selective excitation pulse design algorithm. IEEE Tr Medical Imaging 1991; 10(1):53-65. Also available is the dualband RF pulse described in: Schricker AA, Pauly JM, Kurhanewicz J, Swanson MG, Vigneron DB. Dualband spectral-spatial RF pulses for prostate MR spectroscopic imaging....

Matlab
Rosetta
Yeast Resource Center
NIGMS

Rosetta is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions. The Rosetta software contains multiple functional modules, including Rosetta ab initio, RosettaNMR, RosettaDesign, RosettaDock, Rosetta Fragment Selection, Rosetta Nucleic Acids, RosettaLigand, and more.

Sarcalc
NMR Imaging and Localized Spectroscopy
NIBIB

The SAR calculator (SARcalc) is a header file designed to let you see how much power is actually produced by your sequence.  It can be useful for quick calculations before a study so you do not waste time resetting should the RF monitor trip. You can quickly see how much energy is present, and how long you should make the TR period to minimize heating.

Varian FID
Scalar_voxMediation
Resource for MRI of Neurodegenerative Disorders
NIBIB

scalar_voxMediation is a command line tool that will test for the mediation effect, when the independent variables are scalar and the dependent variables are maps (perfusion, deformation, FA, etc.). It assumes that you have already done a voxel-wise analysis of the simple models, then computes the Sobel test for the mediation effects. Note: This program is no longer supported by the CIND.

Windows
SCIRun
Center for Integrative Biomedical Computing (CIBC)
NIGMS

A PSE for modeling, simulation and visualization of scientific problems.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
Seg3D
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Volume segmentation and processing tool, combining a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
Segger
National Center for Macromolecular Imaging
NIGMS

Volume segmentation tool targeted at Cryo-EM density maps. This is a plugin for Chimera.

Linux, Mac OSX, Windows Aligned FASTA, Aligned NBRF/PIR,...(more)
Segment
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program used K-means cluster analysis to produce a 3 tissue classification from a trio of images (T1-weighted, T2_weighted, and PD-weighted). The clustering procedure is identical to the SAS "Fastclus" procedure. It assumes that all 3 inputs are in register.

Windows HDF
SequenceTree
Center for Magnetic Resonance and Optical Imaging
NIBIB

SequenceTree is an open-source pulse programming environment with a large user community which is growing every day. Many pulse sequences are available for download, including: Spoiled Gradient Echo, Balanced Gradient Echo, Fast Spin Echo, Diffusion, T1p.

Linux
SEQUEST
Yeast Resource Center
NIGMS

A method for performing protein identification & peptide sequencing by utilizing mass spectrometry fragmentation patterns to search protein and nucleotide databases has been developed by our lab Our program, SEQUEST, converts the character-based representation of amino acid sequences in a protein database to fragmentation patterns which are compared against the MS/MS spectrum generated on the target peptide. The algorithm initally identifies amino acid sequences in the database that match the measured mass of the peptide,...

Linux
ShapeTools
Laboratory of Neuro Imaging Resource
NIBIB

The LONI ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines.

Linux, Mac OSX, Windows
ShapeTools Applications
Laboratory of Neuro Imaging Resource
NIBIB

A collection of applications based on the various ShapeTools libraries.

Linux, Mac OSX, Windows Minc OBJ, OFF, PLY,...(more)
ShapeViewer
Laboratory of Neuro Imaging Resource
NIBIB

The LONI ShapeViewer is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java, it can run on a wide variety of computers.

Linux, Unix, Windows GIFTI, Minc OBJ, OFF,...(more)
ShapeWorks
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more)
SHIVA - Synchronized Histological Image Viewing Architecture
Laboratory of Neuro Imaging Resource
NIBIB

The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application. SHIVA can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets.

Sicore
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program transforms a segmented image down to the resolution of spectroscopic imaging (SI) or single voxel spectroscopy data, taking into account the SI point spread function, RF pulse profiles, and metabolite chemical shifts. Tissue type contributions to individual voxels are reported.

Windows HDF
SimianTools
National Center for Biomedical Glycomics (NCBG)
NIGMS

SimianTools is a stand alone application for the postprocessing of glycomics mass spectrometric data annotated with the commercial program SimGlycan.

Windows
SIVIC
Hyperpolarized MRI Technology Resource Center
NIBIB

SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

DICOM
SkyLine
Yeast Resource Center
NIGMS

An advanced windows program for building methods and analyzing data from SRM/MRM targeted proteomics experiments. New release of v0.5 and several videos demonstrating the capabilities and how to use the software.

Windows
SMART
Resource for Quantitative Functional MRI
NIBIB

Statistical Analysis. Downloadable subroutines for a variety of imaging analysis tasks as well as video tutorial on visualization and software useage.

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more)
SpectrumLook
Proteomics Research Resource for Integrative Biology
NIGMS

Allows users to visually browse the MS/MS spectra that led to the peptide identifications, including viewing annotations for the identified b and y ions, plus neutral loss ions where appropriate.

Windows mzXML, Text (.txt)
Spiral MRI Pulse Sequence
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

An MRI pulse sequence with spiral read-out gradients and image reconstruction code. The sequence is written in GE's EPIC pulse programming environment and is available in precompiled format for 5.x and LX platforms. The reconstruction software is precompiled C code. You need to have a GE research agreement to be able to run the sequence on your scanner. To obtain this package, please send email to Gary Glover (gary@lucas.stanford.edu) stating your name, research institute,...

Stimulate
NMR Imaging and Localized Spectroscopy
NIBIB

Multifunctional image analysis tool

Varian FID
structureViz2
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A plugin to Cytoscape that links network visualization in Cytoscape with visualization and analysis of molecular structures in Chimera.

SurfaceWarpTools
Laboratory of Neuro Imaging Resource
NIBIB

The Surface Warping protocol warps a collection of shapes to an atlas, using sets of sulcal contours to guide the warp. The atlas is computed from the contours provided by the user, and the resulting shapes will have anatomically homologous vertices.

Linux, Mac OSX, Windows
SVT - Sub-Volume Thresholding Analysis
Laboratory of Neuro Imaging Resource
NIBIB

SVT is a tool for the Statistical Analysis of Stereotactic Functional Brain Data. The series of 'C' subroutines which comprise the SVT library can be easily incorporated into the user's site specific programs adapted to their particular needs.

Irix
SWIFT
NMR Imaging and Localized Spectroscopy
NIBIB

Sweep imaging with Fourier Transform sequences are available for use at other institutions by MTA agreement with CMRR.

Vnmrj 3.2
T1-rho and T2 processing GUI
Center for Magnetic Resonance and Optical Imaging
NIBIB

This MatLab GUI will assist in processing T1rho- or T2-weighted images to create T1rho or T2 parametric maps. Includes 2D in-plane co-registration Affine algorithms to correct for rigid-body distortions between data sets.

Linux, Mac OSX, Windows DICOM
Tailored Constant Density to Variable Density Spiral
Resource for MRI of Neurodegenerative Disorders
NIBIB

This Matlab program (spiral_vdsn.m) generates a constant density spiral starting from the center of k-space out to a selected portion of k-space, and then switches over to a variable density spiral. In this scheme, only the outer regions of k-space are under-sampled. The program uses a Matlab GUI to generate a user-friendly interface. Inputs to the program include the image matrix size, the field of view, the variable density parameter (alpha) for the outer regions...

Linux, Mac OSX, Windows
TARGETgene
Biomedical Simulations Resource (BMSR)
NIBIB

Identification of mutation drivers, possible therapeutic targets and drug candidates in cancer. The GUI allows users to find, select, and explore identified target genes and compounds. Predictions can be validated via user-defined benchmark or curated cancer genes.

Linux, Mac OSX, Windows Matlab
tcaCALC
Southwestern NMR Center for In Vivo Metabolism
NIBIB

The tcaCALC program performs an isotopomer analysis to estimate relative pathway fluxes in biological systems at metabolic and isotopic steady state.  It is used in 13C labeling studies where biological systems (isolated cells, perfused organs or intact animals) are provided enriched substrate(s), and the labeling of intermediates detected using 13C NMR spectroscopy, mass- and tandem mass spectrometry.  The 13C spectra are collected either directly from intact tissue, such as in the case of perfusions conducted...

Windows
tcaSIM
Southwestern NMR Center for In Vivo Metabolism
NIBIB

The tcaSIM program is a tool for use with labeling studies in intermediary metabolism - primarily those applying 13C NMR spectroscopy, but also for 14C radiolabel studies and 13C mass isotopomer analysis. The simulation has been developed to assist in the design of experiments and to help the user understand the effect of various metabolic states and substrate enrichment levels on labeling patterns.

Windows
TDPortal
National Resource for Translational and Developmental Proteomics
NIGMS

The NRTDP TDPortal is a high-throughput search tool for top-down proteomics data running the Galaxy framework on Northwestern University's Quest HPC Cluster.  Results are generated as .tdReport files which are viewable with the TDViewer application.  Tutorials and protocols to use the new system are available.

Web-Based Thermo Raw
TDViewer
National Resource for Translational and Developmental Proteomics
NIGMS

TDViewer is software for viewing top-down proteomics data acquired on TDPortal.  TDViewer displays the results from a .tdReport file by protein or proteoform and allows the user to filter by false discovery rate (FDR), compare multiple searches and produce reports.

Windows
TimeSeries
Center for Magnetic Resonance and Optical Imaging
NIBIB

TIMESERIES is a plugin for the Extractor program (see above) designed to perform parametric analysis of the hemodynamic response of fMRI data. It can be used to produce parametric maps of such metrics as the time-to-peak, latency, and FWHM of the HRF. It also includes regression to an unbiaseded HRF function, ideal for event-related designs. The software accepts a timeseries of 3D AVW (Analyze) image files as input.

Analyze (.hdr), Analyze (.img.gz),...(more)
tMCimg
Resource for MRI of Neurodegenerative Disorders
NIBIB

tMCimg uses a Monte Carlo algorithm to model the transport of photons through 3D highly volumes with spatially varying optical properties and arbitrary boundary conditions.

Linux, Mac OSX, Windows
Tools for GE MR Data
Center for Advanced Magnetic Resonance Technology at Stanford
NIBIB

Software developed by Marcus Alley (mtalley@stanford.edu). These are all binary programs (so you might have to make them executable after download) that run from a command window.

Topograph
Yeast Resource Center
NIGMS

Topograph is an advanced program for the analysis of proteomics data using stable isotope labeling. This software is still in the early stages of development. Improvements are added regularly.

Windows
ValMap
Resource for MRI of Neurodegenerative Disorders
NIBIB

ValMap is a command line voxel-wise statistical analysis program for images. Images can be gray matter density, jacobian images, etc. The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix. Note: This program is no longer supported by the CIND.

Windows Analyze (.hdr), Analyze (.img.gz),...(more)
Venn Diagram Plotter
Proteomics Research Resource for Integrative Biology
NIGMS

Draws correctly proportioned and positioned two and three circle Venn diagrams whose colors can be customized and the diagrams copied to the clipboard or saved to disk.

Windows mzXML, Text (.txt)
VIPER
Proteomics Research Resource for Integrative Biology
NIGMS

Used to visualize and characterize the features detected during LC-MS analyses.

Decon2LS .CSV files, ICR2LS...(more)
Virtual Tissue Simulator (VTS)
Laser Microbeam and Medical Program
NIBIB

A modular and scalable platform to provide an integrated suite of computational tools to define, solve, visualize, and analyze relevant forward and inverse radiative transport problems in Biomedical Optics.

Linux, Mac OSX, Windows
VMD
Center for Macromolecular Modeling and Bioinformatics
NIGMS

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.  VMD incorporates built-in tools for structure building, simulation analysis, sequence alignment, photorealistic ray tracing, and movie making.  VMD supports multi-core CPUs, parallel computers, and it benefits from GPU-accelerated computing for demanding analysis and visualization computations.

Linux, Mac OSX, Windows AMBER, AMBER "CRD" trajectory...(more)
WAIR - Wavelet Analysis of Image Registration
Laboratory of Neuro Imaging Resource
NIBIB

A tool for the quantitative analysis of various n-dimensional (n-D) image registration techniques. The series of 'C' subroutines which comprise the WAIR library can be easily incorporated into the user's site specific programs and adapted to their particular needs.

Irix
WESTPA
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

WESTPA (the Weighted Ensemble Simulation Toolkit with Parallelization and Analysis) is an open-source software package that provides a high-performance framework for carrying out extended-timescale simulations of rare events with rigorous kinetics using the weighted ensemble algorithm of Huber and Kim (1996). The software also includes options for further enhancing the sampling efficiency through reassignment of weights according to either equilibrium or nonequilibrium steady state, and a plugin for using a weighted ensemble-based string method. The...

Linux, Mac OSX
XNAT in CAWorks
Resource for Quantitative Functional MRI
NIBIB

Imaging Informatics for common management, productivity, and quality assurance for imaging and associated data.

Linux, Mac OSX, Windows VTK (.vtk)
YADA
Yeast Resource Center
NIGMS

YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). YADA also enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.

Jump to Software Resources

Dataset / Database Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
3D coronal Reeler mouse brain
Integrated Center for In Vivo Microscopy
NIBIB

Contrast-enhanced MR scans of fixed perfused mouse brains at 9.4 T.

Linux, Mac OSX, Windows MRI 0 - 500MB
3D MR datasets C57BL/6 mouse embryos
Integrated Center for In Vivo Microscopy
NIBIB

Web-accessible atlas of high-resolution normal, transgenic, and mutant mouse models at embryonic and neonatal stages.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 500MB - 2GB
5-dimensional micro-CT of cardiac cycle
Integrated Center for In Vivo Microscopy
NIBIB

A retrospectively-gated dual energy scan with optimized filters and voltages, and a series of computational operations to reconstruct the data results in 5-dimensional volumetric images that distinguish different materials at different points in time.

Linux, Mac OSX, Windows Binary CT 500MB - 2GB
Adult Wistar rat atlas
Integrated Center for In Vivo Microscopy
NIBIB

MR histology atlas aligned with the Paxinos-Watson atlas, based on optical sections, compares histochemical and immuno-marker data.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 0 - 500MB
Alzheimer's disease mouse model
Integrated Center for In Vivo Microscopy
NIBIB

Automated analyses to produce an unbiased longitudinal view of volumetric changes in a transgenic mouse model for Alzheimer's disease (AD) shows that MR microscopy can expand our view of AD, from the earliest amyloid deposits to the most remote volumetric changes.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 0 - 500MB
Anatomical Image Datasets
Resource for Quantitative Functional MRI
NIBIB

Segmented Subvolumes

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) MRI 0 - 500MB
Aneurysm
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Magnetic resonance angiogram of the vasculature of a patient's head

SCIRun MRA 0 - 500MB
Brain DMW
Center for Integrative Biomedical Computing (CIBC)
NIGMS

MRI scan of a head

Linux, Mac OSX, Windows SCIRun MRI 0 - 500MB
Brain DT
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Twelve diffusion weighted volumes and one non-diffusion-weighted (B=0) reference volume.

NRRD (.nhdr), NRRD (.nrrd) DWI 0 - 500MB
Brain EG
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Comprehensive dataset of a head. This dataset contains a segmented tetrahedral finite element mesh, high- and low-resolution surface models of the scalp and cortex, a point-cloud of electrodes, and a dipole location for a forward simulation.

Linux, Mac OSX, Windows SCIRun EEG 0 - 500MB
Capecchi Mouse Paw
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Mouse paw dataset used to test the Capecchi use case scenario in Seg3D

NRRD (.nhdr), NRRD (.nrrd) CT 0 - 500MB
Convert Examples
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Examples that demonstrate how to use the SCIRun converters.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
CT Atlas of the Abdomen
Neuroimaging Analysis Center
NIBIB

The abdomen atlas was derived from a computed tomography (CT) scan.

CT 0 - 500MB
Cylinder (3-shell)
Center for Integrative Biomedical Computing (CIBC)
NIGMS

This is a 3-shell cylinder model. Each shell has a distinct conductivity index.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Cytoscape App Store
National Resource for Network Biology
NIGMS

The Cytoscape App Store highlights the important features that apps add to Cytoscape, enable researchers to find and install apps they need and help developers promote their apps. Cytoscape provides a solid platform for network visualization and analysis, but it’s really all about the apps. Researchers and developers from institutions around the world have built on top of Cytoscape to add new functionality and tailored solutions for a broad range of network-related projects. The App Store is dedicated to...

Web-Based Database 2GB - 8GB
Developing Wistar rat brain
Integrated Center for In Vivo Microscopy
NIBIB

Developmental neuro-ontology designed specifically to track regional changes in MR biomarkers throughout rat postnatal neurodevelopment.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) MRI 500MB - 2GB
Diffusion Tensor Imaging Databases
Resource for Quantitative Functional MRI
NIBIB

Human Brain Atlas, Normal Human Volunteer Database, Developmental Databases

Analyze (.hdr), Analyze (.img.gz),...(more) DTI 8GB - 16GB
FEM Electrodes
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Simple example datasets that can be used as electrodes in finite element simulations.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
GeneMANIA
National Resource for Network Biology
NIGMS

GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity.

Web-Based BioPAX Database 2GB - 8GB
GlycO
National Center for Biomedical Glycomics (NCBG)
NIGMS

Glycomics Ontology, is an ontology focusing on the representation and storage of glycan structures and other molecules.

Ontology 0 - 500MB
Head and Neck Atlas
Neuroimaging Analysis Center
NIBIB

The head and neck atlas was derived from a reduced resolution (256x256) CT MANIX data set from the OSIRIX data sets.

CT 0 - 500MB
Heart DT
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Diffusion weighted images of the heart.

NRRD (.nhdr), NRRD (.nrrd) DWI 0 - 500MB
Kirby 21
Resource for Quantitative Functional MRI
NIBIB

A multi-modal MRI reproducibility data resource: MPRAGE, FLAIR, DTI, RS fMRI, B0 maps, B1 maps, ASL, VASO, T1 mapping, T2 mapping, Magnetization Transfer

NifTI (.nia), NifTI (.nii,...(more) MRI 2GB - 8GB
map3d
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Various datasets for map3d.

Geometric Model 0 - 500MB
Matlab Examples
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Matlab data contains geometry and potentials for a dog heart. The type of time series data is epicardial potentials. The mesh represents the geometry of 490 sock electrodes.

Matlab Geometric Model 0 - 500MB
Micro-CT for tumor vasculature
Integrated Center for In Vivo Microscopy
NIBIB

Novel post-reconstruction spectral filtration scheme to decompose results into 3D iodine and gold maps to allow simultaneous measurement of extravasated gold and intravascular iodine concentrations. Demonstrates in vivo application to measure fractional blood volume and vascular permeability of active tumor growth over 5 days.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) CT 0 - 500MB
Micro-CT pipeline
Integrated Center for In Vivo Microscopy
NIBIB

Quantitative analysis of 4D cardiac images needs segmentation of cardiac chambers at each time point, which is very time-consuming if done manually. We show a pipeline for registration-based segmentation and functional analysis of 4D cardiac micro-CT mouse data.

Linux, Mac OSX, Windows CT 0 - 500MB
MicroCT Collection
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Collection of 51 small animal microCT scans.

VFF CT 0 - 500MB
Mouse embryos
Integrated Center for In Vivo Microscopy
NIBIB

A genetic marker and novel MR microscopy techniques demonstrate origins of dorsal mesenchymal protrusion in the dorsal mesocardium, and its substantial contribution to atrioventricular septation.

Linux, Mac OSX, Windows TIFF (.tiff, .tif, .TIFF,...(more) Microscopy 0 - 500MB
MR histology data for control and aged rat kidneys
Integrated Center for In Vivo Microscopy
NIBIB

Uses MR histology to determine background pathology in kidneys due to chronic disease, inflammation, or age-related degeneration. Several contrast mechanisms were explored to optimize scanning protocols.

Linux, Mac OSX, Windows MRI MRI 500MB - 2GB
MR-guided Prostate Biopsy pre- and intra-procedural MRI Registration Evaluation Dataset
National Resource Center for Image-Guided Therapy
NIBIB

The dataset contains MRI volumes and additional data collected for 10 patients that underwent MR-guided prostate biopsy.

MRI MRI 0 - 500MB
Multi-modality MRI-based Atlas of the Brain
Neuroimaging Analysis Center
NIBIB

The brain atlas is based on a MRI scan of a single individual.

MRI 0 - 500MB
NA-MIC CARMA Atrial Fibrillation Data
National Resource Center for Image-Guided Therapy
NIBIB

Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: Pre and Post Radiofrequency Ablation LGE-MRI Collection.

MRI 2GB - 8GB
NA-MIC CARMA Longitudinal Left Atrial Shape Data
National Resource Center for Image-Guided Therapy
NIBIB

Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: CARMA Longitudinal Left Atrial Shape Data.

MRI 500MB - 2GB
NA-MIC HD Traveling Human Phantom
Neuroimaging Analysis Center
NIBIB

Traveling Human Phantom: 5 human subjects with >7 MRI scans from different institutions and scanners as well as a ball phantom. (Fill out the form File:NAMIC DATA SHARING.doc to request access.)

MRI N/A
NA-MIC Huntingtons Disease Data
Neuroimaging Analysis Center
NIBIB

A longitudinal collection of MRI scans for Huntingtons subjects. (Fill out the form File:NAMIC DATA SHARING.doc to request access.)

MRI N/A
NCIGT Brain Tumor (Glioma) Resection Data on XNAT
National Resource Center for Image-Guided Therapy
NIBIB

This is a collection of 33 publicly available MR data sets containing brain tumors (gliomas). Each data set contains multiple MR acquisitions (T1, T2, or SPGR) within a single series, as well as a description of the tumor, its size, grade, and location.

MRI 0 - 500MB
NCIGT fMRI for Neurosurgery
National Resource Center for Image-Guided Therapy
NIBIB

This is a collection of 44 publicly available functional mri scans for neurosurgery. The series description is the task performed for that particular series.

fMRI 0 - 500MB
NCIGT IntraOperative Neurosurgical Data on XNAT (Part I)
National Resource Center for Image-Guided Therapy
NIBIB

This is a collection of 101 neurosurgical cases made available by the Image Guided Therapy Program at Harvard-Brigham and Women's Hospital.

MRI MRI 0 - 500MB
NCIGT IntraOperative Neurosurgical Data on XNAT (Part II)
National Resource Center for Image-Guided Therapy
NIBIB

This is a collection of 101 neurosurgical cases made available by the Image Guided Therapy Program at Harvard-Brigham and Women's Hospital.

MRI 0 - 500MB
NDEx
National Resource for Network Biology
NIGMS

NDEx (the Network Data Exchange) is an open source software platform where scientists and organizations can share, store, manipulate and publish biological network knowledge. Users can take advantage of the free Public NDEx Server while companies and organizations can decide to install their own NDEx Server application locally. The NDEx Project is developed in tight association with the Cytoscape project.

Web-Based JSON Database 2GB - 8GB
NeXO
National Resource for Network Biology
NIGMS

NeXO is a gene ontology inferred directly from large-scale molecular networks. A gene ontology provides structured knowledge about the cellular components, processes, and functions encoded by genes. While most ontologies – including the highly successful Gene Ontology Database (GO) – are constructed through manual expert curation, NeXO is a data-driven gene ontology inferred directly from ‘omics data. NeXO (The Network Extracted Ontology) uses a principled computational approach which integrates evidence from hundreds of thousands of individual...

Web-Based Database 2GB - 8GB
NMR Animations
Resource for MRI of Neurodegenerative Disorders
NIBIB

The NMR_Animations Powerpoint (nmr_Animations.pptx) presentation illustrates the vector model for NMR under the action of first, the main magnetic field, and second, an applied off-resonance RF pulse from the viewpoint of the rotating frame.

Linux, Mac OSX, Windows N/A 0 - 500MB
Phenotyping of the mouse heart
Integrated Center for In Vivo Microscopy
NIBIB

4D acquisition with high spatial resolution, high temporal resolution (9.6 ms), and fast acquisition time (16 minutes) allows for rapid measurement of heart function in 3 mouse strains for both left and right ventricular volumes.

Linux, Mac OSX, Windows JPEG (.jpg, .jpeg, .JPG,...(more) MRI 0 - 500MB
Post-natal Wistar rat brain development
Integrated Center for In Vivo Microscopy
NIBIB

MR atlas to analyze regional morphometric changes and variability throughout rat neurodevelopment.

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more) MRI 500MB - 2GB
Pre- and Post-operative Brain Tumor MRI Dataset with Resection
National Resource Center for Image-Guided Therapy
NIBIB

This brain image dataset of pre- and post-resection images was used to generate the data presented in the paper Summarizing and Visualizing Uncertainty in Non-Rigid Registration.

MRI 0 - 500MB
Pseudo-Continuous Arterial spin Labeling
Resource for MRI of Neurodegenerative Disorders
NIBIB

ASL.pptx shows animations of the progression of the magnetization of flowing spins under the action of pseudo-continuous arterial spin labeling (ASL) pulses.  Inversion and two versions of null pulses are shown. The pulses are described in Nezamzadeh, et al. J Magn Reson Imaging 31, 1419, 2010.

Linux, Mac OSX, Windows N/A 0 - 500MB
Public Anonymized Dataset (PAD)
Laboratory of Neuro Imaging Resource
NIBIB

Public anonymized MRI dataset.

MRI N/A
ReferO
National Center for Biomedical Glycomics (NCBG)
NIGMS

Reference Ontology, is an ontology that complements concepts stored in the GlycO ontology with references to external sources (e.g. other database, biological source, publications)

Ontology 0 - 500MB
Registration Image Library
Neuroimaging Analysis Center
NIBIB

Contains example cases of image registration using the Slicer registration tools. Includes multiple modalities (MRI, MR DTI, CT, PET), multiple anatomic structures (brain, thoracic, abdominal), multiple approaches (manual, automated, affine, non-rigid, masking) Includes for each case suggested processing pipeline with stepwise instructions.

Linux, Mac OSX, Windows NRRD (.nhdr), NRRD (.nrrd) MRI 0 - 500MB
SPL Automated Segmentation of Brain Tumors Image Datasets
Neuroimaging Analysis Center
NIBIB

A repository of 10 automated and manual segmentations of meningiomas and low-grade gliomas.

MRI N/A
SPL Knee Atlas
Neuroimaging Analysis Center
NIBIB

The knee atlas was derived from a MRI scan, using semi-automated image segmentation and three-dimensional reconstruction techniques.

MRI N/A
Structure-Function Linkage Database
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A highly curated database of enzyme families/superfamilies and associated sequence-structure-function relationships. Superfamilies are defined by a conserved chemical capability such as a partial reaction, families by a conserved overall reaction.

Database N/A
Time-Dependent
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Time-dependent datasets for use with the tikhonov-inversion, show-eeg-data, and torso-tank-bem, BioPSE networks.

Linux, Mac OSX, Windows Matlab, SCIRun EEG 0 - 500MB
Torsotank 10jan01
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Torsotank experiment. Geometry includes the 490 ventricular electrode sock and the CVRTI torso tank (374 leads). Interventions were controlled flow in left anterior descending artery.

Geometric Model 500MB - 2GB
Torsotank 18dec03
Center for Integrative Biomedical Computing (CIBC)
NIGMS

CVRTI torso tank experiment with 490 lead epicardial sock and 374 lead torso tank. Includes aligned geometry. Interventions included limiting coronary flow and inserting a left ventricular balloon to provide mechanical load.

Geometric Model 0 - 500MB
Torsotank 19jun03
Center for Integrative Biomedical Computing (CIBC)
NIGMS

CVRTI torso tank experiment with 490 lead epicardial sock and 374 lead torso tank. Includes aligned geometry. Interventions included limiting coronary flow and inserting a left ventricular balloon to provide mechanical load. This one also has extensive MRI data.

Geometric Model 500MB - 2GB
Utah Torso
Center for Integrative Biomedical Computing (CIBC)
NIGMS

High resolution geometry of the Utah Torso model. The meshes are tetrahedral volumes, with conductivity tensors stored with the elements. There are ten different conductivity values throughout the volume. The surfaces are TriSurfs and correspond to the boundaries of the distinct conductivity regions.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Utah Torso (low res)
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Low resolution geometry of the Utah Torso model. The meshes are tetrahedral volumes, with conductivity tensors stored with the elements. The surfaces are TriSurfs and correspond to the boundaries of the distinct conductivity regions.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Utah Torso (text based)
Center for Integrative Biomedical Computing (CIBC)
NIGMS

High resolution geometry of the Utah Torso model. The meshes are tetrahedral volumes, with conductivity tensors stored with the elements. There are ten different conductivity values throughout the volume. The surfaces are TriSurfs and correspond to the boundaries of the distinct conductivity regions.

Text (.txt) Geometric Model 0 - 500MB
Waxholm Space comprehensive mouse brain atlas
Integrated Center for In Vivo Microscopy
NIBIB

Normal adult mouse brains acquired at 43-micron isotropic resolution using a streamlined protocol (specimen fixation, staining, image acquisition, reconstruction, and normalization to a common reference space, called Waxholm Space).

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more) MRI 0 - 500MB
Waxholm Space mouse brain atlas (DTI)
Integrated Center for In Vivo Microscopy
NIBIB

Data provides a critical addition to Waxholm Space, our online comprehensive atlas of the mouse brain. Averaged values of DTI indices were computed in 9 white matter structures in each brain.

Linux, Mac OSX, Windows DTI 0 - 500MB
WikiPathways
National Resource for Network Biology
NIGMS

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. Users can browse and edit pathways of interest from dozens of model organisms and download pathways in several formats.

Web-Based BioPAX, JSON Database 500MB - 2GB
YRC Public Data Repository
Yeast Resource Center
NIGMS

Provides access to scientific experimental data resulting from collaborations and technology development involving the YRC. The data has been made public either through publication or by specific consent of the researchers involved. Data include yeast two-hybrid, tandem mass spectrometry, protein complex prediction, and fluorescence microscopy.

Fluorescent Stained Microscopy N/A
YRC Public Image Repository
Yeast Resource Center
NIGMS

A very large database and accompanying web application containing fluorescent microscopy images depicting the localization, co-localization and FRET (fluorescence energy transfer) of proteins in cells--particularly in the budding yeast Saccharomyces cerevisiae.

Fluorescent Stained Microscopy N/A