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https://www.janelia.org/project-team/mouselight

Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.

Proper citation: MouseLight Project (RRID:SCR_016668) Copy   

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https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

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https://github.com/afids

Open framework for evaluating correspondence between brain images and teaching neuroanatomy.

Proper citation: AFIDs (RRID:SCR_016623) Copy   

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http://portal.brain-map.org/

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

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http://dabi.loni.usc.edu/

Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.

Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy   

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http://www.tbi-impact.org/

Project focused on advancing knowledge of prognosis, trial design and treatment in Traumatic Brain Injury. IMPACT has developed and validated prognostic models for classification and characterization of TBI series, and participated in development of standardization of data collection in TBI studies.

Proper citation: IMPACT: International Mission for Prognosis and Analysis of Clinical Trials in TBI (RRID:SCR_000539) Copy   

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http://database.hudsen.eu/

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   

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http://neurosynth.org

Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.

Proper citation: NeuroSynth (RRID:SCR_006798) Copy   

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http://cmbn-approd01.uio.no/nesys/

Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.

Proper citation: Functional Anatomy of the Cerebro-Cerebellar System (FACCS) (RRID:SCR_001661) Copy   

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http://qnl.bu.edu/obart

Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases.

Proper citation: OBART (RRID:SCR_001903) Copy   

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http://www.cogsci.ucsd.edu/index.php

This UCSD department, the first Cognitive Science Department in the world, provides a focus for the continued evolution of the discipline of cognitive science. Cognitive science is a diverse field unifying three broad categories: the brain, behavior and computation. It's the study of how people, animals and computers think, act and learn. In order to understand the mind/brain, cognitive science brings together the methods and discoveries from neuroscience, psychology, linguistics, anthropology, philosophy and computer science. The interdisciplinary aspects of cognitive science continue to flourish, and the participation of the broader cognitive science community on campus continues to be fundamental to cognitive science as practiced at UCSD. The interdisciplinary Ph.D. program continues to be offered as a degree option (in addition to the departmental Ph.D.), with participation by members of the Departments of Anthropology, Biology, Cognitive Science, Communication, Computer Science and Engineering, Linguistics, Music, Neuroscience, Philosophy, Psychiatry, Psychology, and Sociology. Cognitive Science is a relatively young field that focuses on conducting new research into the field or applying existing knowledge into new applications. This Department contains several research labs each specializing in different areas and the Department's faculty has also been published many times in various publications. Sponsors: This department is supported by the University of California at San Diego.

Proper citation: UCSD Cognitive Science: The Future of Cognitive Science (RRID:SCR_001926) 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   

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http://flybrain.stanford.edu/

Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.

Proper citation: Flybrain at Stanford (RRID:SCR_001877) Copy   

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http://nips.cc/

The Neural Information Processing Systems (NIPS) Foundation is a non-profit corporation whose purpose is to foster the exchange of research on neural information processing systems in their biological, technological, mathematical, and theoretical aspects. Neural information processing is a field which benefits from a combined view of biological, physical, mathematical, and computational sciences. The primary focus of the NIPS Foundation is the presentation of a continuing series of professional meetings known as the Neural Information Processing Systems Conference, held over the years at various locations in the United States and Canada.

Proper citation: NIPS - Neural Information Processing Systems Conference (RRID:SCR_001998) Copy   

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http://dynamicbrain.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19. 2022. Platform to promote studies on dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Provides services such as data sets, popular research findings and articles and current developments in field. This site has been archived since FY2019 and is no longer updated.

Proper citation: Dynamic Brain Platform (RRID:SCR_001754) Copy   

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http://www.yerkes.emory.edu/

Center for advancing scientific understanding and improving the health and well-being of humans and nonhuman primates. The Center conducts research in microbiology and immunology, neurologic diseases, neuropharmacology, behavioral, cognitive and developmental neuroscience, and psychiatric disorders.

Proper citation: Yerkes National Primate Research Center (RRID:SCR_001914) Copy   

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http://bmi.neuroinf.jp/

Databases of accumulating BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. Databases include: # Database of BMI (Brain Machine Interfaces)-related papers: More than 3500 BMI-related papers are registered. Each paper has original tags, for example, recording method and subject, for easy searching. # Database of original contents: BMI-related materials (Movie, Picture, Data, Program) provided by scientists. # Database of BMI-related research sites: 185 BMI-related research sites in the world (university, institute and company) are registered. The research site can be searched either by the location using clickable map or by the field of interest. # Database of BMI-related materials: Links to BMI-related materials (Movie, Picture, Document, Data, Program) are listed. You can easily find materials of your interest since each material is classified into research field. # BMI-related column: The columns are written by researchers specialized in BMI. Original contents include: * Neuronal activity during performance of a memory-guided movement * Reconstructed visual images from human fMRI activity * fMRI data and program for visual image reconstruction * Brain sections of monkeys, stained for several gene markers * Cortical Box Method: The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis. * Multineuron activity in monkey prefrontal cortex * Monkey Atlas: **Brain sections of monkeys, stained for AChE, ER81 mRNA and Sema3E mRNA - These pictures are low-resolution photos of serial brain sections of monkeys, stained for AChE as well as for ER81 and Sema3E mRNAs. The compressed file contains JPEG photos and html files for web browser navigation. Other materials are available at our website BraInSitu dedicated for in situ hybridization resources for brains. BraInSitu http://www.nibb.ac.jp/brish/indexE.html ** MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages - MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages ** The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey - The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey * Monkey M1 BMI ** m-file for checking the results of wrist angle estimation- This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/uln ** m-file for training of wrist angle estimation -This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation.ar deviation. ** M1 Neuronal Activity during monkey performing a motor task - video/x-ms-wmv ** Muscle tension - To estimate muscle tension from raw emg signal ** raw EMG signal - Raw EMG signal for 5 seconds ** training data of wrist angle and emg signal - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. ** Weight file of neural network - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. * Multineuron activity in monkey prefrontal cortex: Multineuron activity in monkey prefrontal cortex recorded by 3 tetrodes. Vertical 4 lines indicate one tetrode. Adjacent tetrodes are around 500 micron apart to each other.

Proper citation: Brain Machine Interface Platform (RRID:SCR_001813) Copy   

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http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html

Set of programs and Tk/Tcl scripts, with a GUI wrapper, for extracting the inner and outer cortical surfaces from a T1-weighted MR image of the human brain. It is based on the TFI C++ library and is written for a Unix-based environment (specifically 64-bit and 32-bit versions of Ubuntu). As a courtesy to Apple users a version for Apple/X11 is maintained but the OS X version will always lag the Linux version; also, because some of the third-party libraries SurfRelax relies on may not be supported in or compatible with future versions of OS X, there is no guarantee that the OS X version will be supported indefinitely. Although in principle SurfRelax could be run under Windows (using Cygwin), because of the difficulties of maintaining multiple platforms and the limited support libraries available under Cygwin, there will no longer be support for SurfRelax on this platform. The surfaces are guaranteed to be topologically equivalent to a sphere, thereby obviating the need for handle removal. SurfRelax requires no user intervention, although minor manual editing is recommended for optimal results (normally less than 10 minutes per hemisphere). SurfRelax has several properties that compare favorably with other software packages for surface reconstruction: * Free software - The binaries (written in C++ and Tcl/Tk) are in the public domain. The source code will be released once legacy code issues have been resolved (i.e. replacing with GPL code). * Uses standard public file formats: Analyze file format (SPM/FSL-compatible) for volumes and OOGL OFF binary format for surfaces (see www.geomview.org (http://www.geomview.org/docs/html/geomview_26.html#OOGLRef)) * Combines advantages of volumetric and surface-based methods for surface generation * Correct topology of output surface guaranteed * Requires little or no user intervention - no need for manual handle removal * Relatively robust to noise - multi-scale method compensates for partial volume effects and intensity inhomogeneities * Relatively fast (an entire brain is segmented, extracted and unfolded in less than 2 hours of CPU time) * Powerful editing and visualization tools for volumes and surfaces * Readily extendable - for instance for use with monkey brains or children's brains * Can be used to visualize functional data from SPM or FSL * Includes tools for integration with Stanford's VISTASOFT tools for FMRI data analysis (white.stanford.edu)

Proper citation: SurfRelax (RRID:SCR_002139) Copy   

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http://www.bioon.com/bioline/neurosci/course/index.htm

An illustrated guide to the essential basics of clinical neuroscience created in conjunction with the first-year course for medical students.
Topics covered:
* Coronal and horizontal sections
* Basic visual pathway
* Basic somatosensory pathway
* Basic motor pathway
* Eye and retina
* Central visual pathways
* Auditory and vestibular systems
* Somatosensory pathways from the body
* Somatosensory pathways from the face
* Spinal motor structures
* Brainstem nuclei of cranial nerves
* Basal ganglia and cerebellum
* Hypothalamus and autonomic nervous system
* Medial temporal lobe and memory
* Sleep and language
* Where is...?

Proper citation: Washington University School of Medicine Neuroscience Tutorial (RRID:SCR_002271) Copy   

•   Source: SciCrunch Registry

http://connectomes.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.

Proper citation: Connectomes.org (RRID:SCR_002243) Copy   

•   Source: SciCrunch Registry