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https://github.com/csitron/Microscopy_tif_Channel_Quant_MATLAB

Software application for quantification of fluorescence channel area in TIFF images using MATLAB.

Proper citation: Microscopy_tif_Channel_Quant_MATLAB (RRID:SCR_026999) Copy   

•   Source: SciCrunch Registry

https://www.car-net.org/tools

Software function as Matlab implementation of the TFA as specified in the White Paper (2015). An example of use on the supplied data (tfa_sample_data.txt) is given in tfa_demo.m and results are reported at the end of this report.

Proper citation: CARNet TFA Function (RRID:SCR_027022) Copy   

•   Source: SciCrunch Registry

https://github.com/lrq3000/auto_acpc_reorient/

Software tool as cross platform automatic AC-PC realignment,reorientation and coregistration robust to brain damage, using template matching in SPM12. Provides two new tools auto_acpc_reorient and auto_acpc_coreg using toolbox Statistical Parametric Mapping 12 to reorient and coregister structural, functional and other modalities of MRI volumetric brain images.

Proper citation: auto_acpc_reorient (RRID:SCR_018308) Copy   

•   Source: SciCrunch Registry

https://github.com/cochran4/GEMB

Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.

Proper citation: GEMB (RRID:SCR_018904) Copy   

•   Source: SciCrunch Registry

https://github.com/treder/MVPA-Light

Software Matlab based MVPA toolbox for EEG and MEG analyses. Classification and regression toolbox for multi dimensional data. Performs cross validation, hyperparameter tuning, and nested preprocessing. Computes various classification and regression metrics and establishes their statistical significance.

Proper citation: MVPA Light (RRID:SCR_022173) Copy   

•   Source: SciCrunch Registry

https://github.com/fahrenfort/ADAM

Software Matlab based MVPA toolbox for EEG analyses. Allows direct comparison of ERP/ERF results to MVPA results using any dataset in standard EEGLAB or Fieldtrip format. Performs and visualizes multiple comparison corrected group decoding and forward encoding results in variety of ways, such as classifier performance across time, temporal generalization (time-by-time) matrices of classifier performance, channel tuning functions (CTFs) and topographical maps of (forward-transformed) classifier weights.

Proper citation: Amsterdam Decoding And Modeling (RRID:SCR_022172) Copy   

•   Source: SciCrunch Registry

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

A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.

Proper citation: MRIcroS (RRID:SCR_014142) Copy   

•   Source: SciCrunch Registry

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

Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.

Proper citation: GIMME (RRID:SCR_014115) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/MrDiffusion

Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MrDiffusion (RRID:SCR_016567) Copy   

•   Source: SciCrunch Registry

http://www.uimcimes.es/contenidos/golink?p=1

Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.

Proper citation: QModeling (RRID:SCR_016358) Copy   

•   Source: SciCrunch Registry

http://brainarchitecture.org/allen-atlas-brain-toolbox

Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.

Proper citation: Brain Gene Expression Analysis toolbox (RRID:SCR_017438) Copy   

•   Source: SciCrunch Registry

http://www.nisox.org/Software/SwE/

Software tool as SPM extension for longitudinal and repeated measures data. Modelling of longitudinal and repeated measures neuroimaging data.Implemented as Matlab toolbox for SPM8 or SPM12.

Proper citation: Sandwich Estimator Toolbox (RRID:SCR_019279) Copy   

•   Source: SciCrunch Registry

https://github.com/kristinbranson/BABAM

Graphical user interface for exploring hypotheses of correlations between neural activity in regions of the brain and behavior for Drosophila melanogaster. These correlation hypotheses are the result of our thermogenetic neural activation screen from the Janelia GAL4 collection.

Proper citation: BABAM (RRID:SCR_015632) Copy   

•   Source: SciCrunch Registry

http://www.spisop.org

Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel.

Proper citation: SpiSOP (RRID:SCR_015673) Copy   

•   Source: SciCrunch Registry

http://fmatoolbox.sourceforge.net

Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.

Proper citation: FMAToolbox (RRID:SCR_015533) Copy   

•   Source: SciCrunch Registry

http://www.rutishauserlab.org/osort

Framework for spike sorting that includes tools for pre-processing, spike detection, spike sorting, and sorting quality evaluation. It is principally designed for sorting of single-wire microwire recordings in humans, but is being used for other types of recordings as well.

Proper citation: OSort (RRID:SCR_015869) Copy   

•   Source: SciCrunch Registry

http://soundanalysispro.com/

Software for birdsong analysis that performs automated recording and analysis of animal vocalization. It can record, analyze and manage sound data over prolonged periods.

Proper citation: Sound Analysis Pro (RRID:SCR_016003) Copy   

•   Source: SciCrunch Registry

http://fmri.uib.no/index.php?option=com_content&view=article&id=53&Itemid=78

Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts.

Proper citation: The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) Copy   

•   Source: SciCrunch Registry

https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pubmed/23489480

Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.

Proper citation: MicroFilament Analyzer (RRID:SCR_016411) Copy   

•   Source: SciCrunch Registry