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http://www.virtualflybrain.org

An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

Proper citation: Virtual Fly Brain (RRID:SCR_004229) Copy   

•   Source: SciCrunch Registry

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

Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.

Proper citation: UNC Human Brain Atlas (RRID:SCR_002606) Copy   

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http://www.epmba.org/

The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07).

Proper citation: EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas (RRID:SCR_001882) Copy   

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http://www.gensat.org/retina.jsp

Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.

Proper citation: Retina Project (RRID:SCR_002884) Copy   

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http://www.mouseconnectome.org/

Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse.

Proper citation: Mouse Connectome Project (RRID:SCR_004096) Copy   

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http://zebrafinch.brainarchitecture.org/

Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies.

Proper citation: Zebrafinch Brain Architecture Project (RRID:SCR_004277) Copy   

•   Source: SciCrunch Registry

http://www.youtube.com/user/WholeBrainCatalog?feature=autoshare

Videos uploaded to YouTube by the Whole Brain Catalog.

Proper citation: WholeBrainCatalog's Channel - YouTube (RRID:SCR_005436) Copy   

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http://cmrm.med.jhmi.edu/cmrm/atlas/human_data/file/JHUtemplate_newuser.html

DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.

Proper citation: DTI White Matter Atlas (RRID:SCR_005279) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.youtube.com/user/sfnvideo

The Society for Neuroscience (SfN) is a nonprofit membership organization of scientists and physicians who study the brain and nervous system. SFNVideo - YouTube are videos uploaded to YouTube by the Society for Neuroscience (SfN). Since inception in 1969, the Society has grown from 500 members to more than 41,000. Today, SfN is the world''s largest organization of scientists and physicians devoted to advancing understanding of the brain and nervous system.

Proper citation: sfnvideo - YouTube (RRID:SCR_005463) Copy   

•   Source: SciCrunch Registry

https://www.youtube.com/user/iniusc

Videos uploaded to YouTube by the Laboratory of Neuro Imaging (LONI). The Laboratory of Neuro Imaging at UCLA strives to improve our understanding of the brain in health and disease. LONI is a leader in the development of advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function.

Proper citation: Laboratory of Neuro Imaging - YouTube (RRID:SCR_005462) Copy   

•   Source: SciCrunch Registry

http://www.brainnav.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.

Proper citation: BrainNavigator (RRID:SCR_008289) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://coins.mrn.org/

A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.

Proper citation: Mind Research Network - COINS (RRID:SCR_000805) Copy   

•   Source: SciCrunch Registry

http://www.loni.ucla.edu/~thompson/thompson.html

The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities.

Proper citation: University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson (RRID:SCR_001924) Copy   

•   Source: SciCrunch Registry

http://sig.biostr.washington.edu/projects/MindSeer/index.html

A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).

Proper citation: MindSeer (RRID:SCR_003019) Copy   

•   Source: SciCrunch Registry

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

Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images.

Proper citation: TumorSim (RRID:SCR_002604) Copy   

•   Source: SciCrunch Registry

Issue

https://github.com/spm

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   

•   Source: SciCrunch Registry

http://humanconnectome.org/connectome/connectomeDB.html

Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source.

Proper citation: ConnectomeDB (RRID:SCR_004830) Copy   

•   Source: SciCrunch Registry