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Software package for p value based multiple testing that also implements dependence test and p-value simulation.
Proper citation: Myriads (RRID:SCR_017447) Copy
https://miracl.readthedocs.io/en/latest/
Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation.
Proper citation: MIRACL (RRID:SCR_020945) Copy
https://github.com/fsotoc/FaReT
Software toolkit of three dimensional models and software to study face perception. Collection of plugins used with MakeHuman to create face stimuli for experiments.
Proper citation: Face Research Toolkit (RRID:SCR_023322) Copy
https://github.com/parklab/NGSCheckMate
Software package for validating sample identity in next generation sequencing studies within and across data types. Used for identifying next generation sequencing data files from the same individual. Used for checking sample matching for NGS data.
Proper citation: NGSCheckMate (RRID:SCR_022994) Copy
https://github.com/Cai-Lab-at-University-of-Michigan/nTracer
Software tool as plug-in for ImageJ software. Used for tracing microscopic images.
Proper citation: nTracer (RRID:SCR_023032) Copy
https://CRAN.R-project.org/package=TrumpetPlots
Software R package to visualize relationship between allele frequency and effect size in genetic association studies.
Proper citation: TrumpetPlots (RRID:SCR_023742) Copy
https://github.com/mne-tools/mne-bids/
Software Python package to link Brain Imaging Data Structure and MNE-Python software for analyzing neurophysiology data with goal to make analyses faster to code, more robust to errors, and easily shareable with colleagues. Provides programmable interface for BIDS datasets in electrophysiology with MNE-Python. Used for organizing electrophysiological data into BIDS format and facilitating their analysis.
Proper citation: MNE-BIDS (RRID:SCR_018766) Copy
http://www.nimh.nih.gov/labs-at-nimh/research-areas/research-support-services/hbcc/index.shtml
A collection of brain tissue from individuals suffering from schizophrenia, bipolar disorder, depression, anxiety disorders, and substance abuse, as well as healthy individuals. The research mission of the NIMH Brain Bank is to better understand the underlying biological mechanisms and pathways that contribute to schizophrenia and other neuropsychiatric disorders, as well as to study normal human brain development.
Proper citation: NIMH Brain Tissue Collection (RRID:SCR_008726) Copy
https://github.com/denisecailab/minian
Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.
Proper citation: Minian (RRID:SCR_022601) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ''''c'''' for continuous, ''''pb'''' for binned point processes, and ''''pt'''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data.
Proper citation: Chronux (RRID:SCR_005547) Copy
https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas
Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression.
Proper citation: Allen Brain Cell Atlas (RRID:SCR_024440) Copy
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases
Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.
Proper citation: Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) Copy
Interactive digital atlas and movies comprising 3-D reconstructions at all stages of human development from Carnegie Stage 12 (CS12; ~26 days post conception (dpc)) to CS23 (~ 56 dpc) and anatomical annotations of the 3-D models linked to an anatomical database. The 3D models are generated using Optical Projection Tomography (OPT; Sharpe et al 2002). The digital atlas is also linked to a gene expression database that has been developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). In the future, the HUDSEN EADHB aims to provide the wider scientific and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes in the developing human brain.
Proper citation: HUDSEN Electronic Atlas of the Developing Human Brain (RRID:SCR_002056) Copy
http://www.nitrc.org/projects/frats/
Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.
Proper citation: Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) Copy
Portal for NIH, NIMH, and NINDS scientific and computer resources including Mac sites, PC sites, Linux sites, intramural programs, intranet and the NIH JumpStart and Directory.
Proper citation: Research Services Branch National Institutes of Mental Health (RRID:SCR_001633) Copy
http://www.nitrc.org/projects/rmdtitemplate/
A population-specific DTI template for young adolescent Rhesus Macaque (Macaca mulatta) monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Their DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that their DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.
Proper citation: DTI-TEMPLATE-RHESUS-MACAQUES (RRID:SCR_002482) Copy
Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression.
Proper citation: NeuroExpresso (RRID:SCR_015724) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 6,2026. Platform for mediation and integration of schizophrenia neuroimaging-related databases. It provides access to federated databases, novel mediation software, and large-scale data-sharing features.
Proper citation: SchizConnect (RRID:SCR_015766) Copy
http://sccn.ucsd.edu/fmrlab/index.html
A Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessary processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure. Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially independent components of the entire data set from the higher-order statistics of the data themselves. FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux. FMRLAB Features * Graphic user interface * Flexible data importing * Interactive data plotting * Computationally efficient * Defined FMRI data structure * Independent component browser * Smooth, transparent component exporting and spatial normalization process * Interface with other software for further analysis or visualization. * SPM-style component plots (MIP, 2-D slice overlay and 3-D)
Proper citation: FMRLAB (RRID:SCR_005164) Copy
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