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http://www.nitrc.org/projects/laplacebeltrami/

A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface.

Proper citation: Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ap_seg_2013_nih/

A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet.

Proper citation: NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) Copy   

•   Source: SciCrunch Registry

http://neurodata.io/

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

Proper citation: neurodata (RRID:SCR_014264) Copy   

•   Source: SciCrunch Registry

http://netpyne.org/

Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.

Proper citation: NetPyNE (RRID:SCR_014758) Copy   

•   Source: SciCrunch Registry

http://www.itk.org

Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Proper citation: Insight Segmentation and Registration Toolkit (RRID:SCR_001149) Copy   

•   Source: SciCrunch Registry

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php

A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation

Proper citation: Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) Copy   

•   Source: SciCrunch Registry

http://neuroimage.usc.edu/brainstorm/

Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

Proper citation: Brainstorm (RRID:SCR_001761) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/itk-snap/

Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Proper citation: ITK-SNAP (RRID:SCR_002010) Copy   

•   Source: SciCrunch Registry

https://github.com/trendscenter/gift

Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki.

Proper citation: Group ICA of fMRI Toolbox (RRID:SCR_001953) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/MultiPhase-SEG

A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed.

Proper citation: MultiPhase-SEG (RRID:SCR_008275) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/DSM

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. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats.

Proper citation: DualSurfaceMin (RRID:SCR_008278) Copy   

•   Source: SciCrunch Registry

http://loni.usc.edu/Software/SVT

Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software.

Proper citation: Sub-Volume Thresholding Analysis (RRID:SCR_008272) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rician_Noise_Removal

Two Slicer3 modules removing rician noise in diffusion tensor MRI

Proper citation: Slicer3 Module Rician noise filter (RRID:SCR_009614) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/BrainParser

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) 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.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/trac/OpenElectrophy

Software Python module for electrophysiology data analysis.

Proper citation: OpenElectrophy (RRID:SCR_000819) Copy   

•   Source: SciCrunch Registry

http://mialab.mrn.org/software/eegift/index.html

Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.

Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy   

•   Source: SciCrunch Registry

https://github.com/UCSFBiomagneticImagingLab/nutmeg

Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.

Proper citation: NUTMEG (RRID:SCR_002748) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/eons/

Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux.

Proper citation: EONS (RRID:SCR_002979) Copy   

•   Source: SciCrunch Registry

http://www.xnat.org

Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data.

Proper citation: XNAT - The Extensible Neuroimaging Archive Toolkit (RRID:SCR_003048) Copy   

•   Source: SciCrunch Registry

https://bioimagesuiteweb.github.io/webapp/index.html

Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

Proper citation: BioImage Suite (RRID:SCR_002986) Copy   

•   Source: SciCrunch Registry