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https://github.com/bids-standard/bids-validator
Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure.
Proper citation: BIDS Validator (RRID:SCR_017255) Copy
http://www.nitrc.org/projects/brainlife_io/
Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.
Proper citation: brainlife.io (RRID:SCR_016513) Copy
https://www.med.upenn.edu/sbia/brats2017.html
Organization that provides a conference about the methods for the segmentation of brain tumors in magnetic resonance imaging (MRI) scans. Its conferences utilize multi-institutional pre-operative MRI scans and focus on the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas.
Proper citation: BraTS (RRID:SCR_016214) Copy
Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks.
Proper citation: Mouse Connectome Project (RRID:SCR_017313) Copy
Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.
Proper citation: Compilation of Genetics Resource Databases (RRID:SCR_017501) Copy
https://github.com/nipy/heudiconv
Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts.
Proper citation: HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) Copy
Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide.
Proper citation: Mononucleotide Repeat Frameshift Portal (RRID:SCR_021125) Copy
A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.
Proper citation: aBEAT (RRID:SCR_002238) 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
http://www.research.va.gov/programs/tissue_banking/als/
A human tissue bank that collects, processes, stores and gives out research specimens for future scientific studies. Presently, the VABBB is obtaining neurologic tissue specimens from Veterans who suffer from amyotrophic lateral sclerosis (ALS) and other illnesses that affect Veterans, along with relevant clinical data, essential for research. Currently, neither the cause nor prevention of ALS is known. Medical researchers are currently examining environmental, toxic, genetic, traumatic, medical, and occupational influences as possible contributors to the development and progression of ALS. Veterans have a higher risk of developing ALS compared with non-Veterans; however, the reasons for this higher risk are currently unknown. Any Veteran with ALS in the U.S. may enroll in the VABBB.
Proper citation: VA Biorepository Brain Bank (RRID:SCR_006546) Copy
Mission of the School of Behavioral and Brain Sciences is to understand the intersection of mind, brain and behavior; enhance the health, education, and quality of life of children and families; and create and implement technologies and therapies that repair and strengthen human abilities. The School is housed in Green Hall on the main UT Dallas campus in Richardson. It also has satellite research centers and facilities in downtown Dallas.
Proper citation: University of Texas at Dallas School of Behavioral and Brain Sciences (RRID:SCR_004645) Copy
Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.
Proper citation: CRCNS (RRID:SCR_005608) Copy
https://www.bminds.brain.riken.jp/
Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus), prepared from histological sections of the marmoset brain using various staining techniques.
Proper citation: Digital Brain Atlas of the Common Marmoset (RRID:SCR_005069) Copy
http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html
V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.
Proper citation: V3D (RRID:SCR_008646) 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
Brain tissue donation program at the UT Southwestern Memory Clinic that aims to utilize these contributions for research on Alzheimer's. Diagnosis of Alzheimer's disease or other dementias are made through autopsy, the results of which are available to family members.
Proper citation: UT Southwestern ADC Brain Tissue Donation Program (RRID:SCR_008837) Copy
Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.
Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy
http://caprica.genetics.kcl.ac.uk/BRAINEAC/
Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders.
Proper citation: Braineac (RRID:SCR_015888) Copy
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
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
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