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Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
https://www.aplysia.earth.miami.edu/
Center where Aplysia californica are cultured and raised for research purposes. Aplysia from the facility serve in research on genomics, human brain function, toxicology for developmental studies, natural products, chemistry for isolation of novel anti-tumor and antibacterial compounds, in the study of transport by digestive tissues and have potential for use in studies of substance addiction and nerve senescence and regeneration.
Proper citation: National Resource for Aplysia (RRID:SCR_008361) Copy
https://www.amazon.com/How-Brain-Works-Mark-Dubin/dp/0632044411
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Is the Brain (Like) a Computer is an e-book written by Prof. Mark Dubin. It consists of the following: Introduction. Why do we consider the relationship of brains and computers and what does this have to do with consciousness? What's a Brain Made Of? A thought experiment. Test Drive a Turing Machine. A theoretical approach. Interim Summary. Many of the main pages have links to additional information. When you click on one of those links a NEW page will open ON TOP of the page you are clicking from. This convention is adopted so that you can look at the additional information and then easily return to the main page you got there from.
Proper citation: Is the Brain (Like) a Computer (RRID:SCR_008809) Copy
http://hdbase.org/cgi-bin/welcome.cgi
A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models
Proper citation: HDBase (RRID:SCR_007132) Copy
http://research.mssm.edu/cnic/
Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies
Proper citation: Computational Neurobiology and Imaging Center (RRID:SCR_013317) Copy
Research forum portal to address brain status by acquiring comprehensive, multimodal data from healthy humans across the lifespan to characterize brain status, assess its change over time, and associate composite descriptors of brain status. Specifically, the measurements are acquired noninvasively by existing neuroimaging technologies (structural MRI, functional MRI, magnetic resonance spectroscopy, diffusion MRI, and magnetoencephalography); in addition, genetic, cognitive, language, and lifestyle data are acquired. Goals: * Derive the Brain Health Index- An integrative assessment of brain status derived from multimodal measurements of brain structure, function, and chemistry. * Continue acquiring data to construct the first-ever databank on brain, cognitive, language and genetic measurements for healthy people across the lifespan. * Provide a novel and unique dataset by which to: characterize brain status, assess its change over time, and associate it with genetic makeup, cognitive function, and language abilities. * Forecast future brain health and disease based on current measurements and guide physicians towards new interventions and evaluate interventions as they develop. * Extend to siblings and other family members to further assess the genetic influences and inheritability.
Proper citation: HBP: Healthy Brain Project (RRID:SCR_013137) Copy
https://github.com/NOCIONS/letswave6/wiki/Download-and-setup
Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.
Proper citation: Letswave (RRID:SCR_016414) Copy
http://www.nitrc.org/projects/nutil/
Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow.
Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy
http://hpc-bioinformatics.cineca.it/stress_mice/
Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data.
Proper citation: Stress Mice Portal (RRID:SCR_017572) Copy
http://ml-neuronbrowser.janelia.org/
Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions.
Proper citation: MouseLight Neuron Browser (RRID:SCR_016669) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
http://www.dartmouth.edu/~rswenson/Atlas/
On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV)
Proper citation: Atlas of the Brain (RRID:SCR_005967) Copy
A blog by Zen Faulkes, an invertebrate neuroethologist at The University of Texas-Pan American.
Proper citation: NeuroDojo (RRID:SCR_006237) Copy
http://neurocritic.blogspot.com/
The Neurocritic is a blog deconstructing the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology. Born in West Virginia in 1980, The Neurocritic embarked upon a roadtrip across America at the age of thirteen with his mother. She abandoned him when they reached San Francisco and The Neurocritic descended into a spiral of drug abuse and prostitution. At fifteen, The Neurocritic''s psychiatrist encouraged him to start writing as a form of therapy.
Proper citation: Neurocritic (RRID:SCR_006528) Copy
http://www.civm.duhs.duke.edu/neuro2012ratatlas/
Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.
Proper citation: Adult Wistar Rat Atlas (RRID:SCR_006288) Copy
https://sites.google.com/site/bipolardatabase/
Database of 141 studies which have investigated brain structure (using MRI and CT scans) in patients with bipolar disorder compared to a control group. Ninety-eight studies and 47 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.
Proper citation: Bipolar Disorder Neuroimaging Database (RRID:SCR_007025) Copy
http://cocomac.g-node.org/main/index.php?
Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.
Proper citation: CoCoMac (RRID:SCR_007277) Copy
Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.
Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) Copy
http://bioinformatics.istge.it/cldb/indexes.html
Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.
Proper citation: Hyper Cell Line Database (RRID:SCR_007730) Copy
https://ndriresource.org/for-researchers/services-capabilities-sample/htorr
NDRI’s Human Tissue and Organs for Research Resource (HTORR) Program has been funded by the National Institutes of Health (NIH) for over 30 consecutive years to support research programs across multiple disciplines. It is through the HTORR program that NDRI provides academic biomedical investigators with donated normal and diseased human tissues and organs recovered from a diverse donor pool using customized procurement, processing, and preservation and distribution protocols. Our HTORR Program supports academic biomedical research investigators needs by providing: Access to a wide array of human biospecimens from any body system * Customized procurement in a variety of preservation formats including fresh, frozen, and fixed suitable for various analytical techniques * Reduced costs for tissue procurement * Technical support to design your studies utilizing human biospecimens * Letters of support and budgetary information for grant applications
Proper citation: Human Tissue and Organ for Research Resource (HTORR) (RRID:SCR_002859) Copy
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