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http://brainarchitecture.org/

Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

Proper citation: Brain Architecture Project (RRID:SCR_004283) Copy   

•   Source: SciCrunch Registry

http://www.brainarchitecture.org/mouse-home

An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset.

Proper citation: Mouse Brain Architecture Project (RRID:SCR_004683) Copy   

•   Source: SciCrunch Registry

https://bams1.org/ontology/viewer.php

Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts.

Proper citation: BAMS Neuroanatomical Ontology (RRID:SCR_004616) Copy   

•   Source: SciCrunch Registry

http://mindboggle.info/data.html

Complete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world! http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full

Proper citation: Mindboggle-101 atlases (RRID:SCR_002439) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases

3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.

Proper citation: UNC Infant 0-1-2 Atlases (RRID:SCR_002569) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/odormapdb

OdorMapDB is designed to be a database to support the experimental analysis of the molecular and functional organization of the olfactory bulb and its basis for the perception of smell. It is primarily concerned with archiving, searching and analyzing maps of the olfactory bulb generated by different methods. The first aim is to facilitate comparison of activity patterns elicited by odor stimulation in the glomerular layer obtained by different methods in different species. It is further aimed at facilitating comparison of these maps with molecular maps of the projections of olfactory receptor neuron subsets to different glomeruli, especially for gene targeted animals and for antibody staining. The main maps archived here are based on original studies using 2-deoxyglucose and on current studies using high resolution fMRI in mouse and rat. Links are also provided to sites containing maps by other laboratories. OdorMapDB thus serves as a nodal point in a multilaboratory effort to construct consensus maps integrating data from different methodological approaches. OdorMapDB is integrated with two other databases in SenseLab: ORDB, a database of olfactory receptor genes and proteins, and OdorDB, a database of odor molecules that serve as ligands for the olfactory receptor proteins. The combined use of the three integrated databases allows the user to identify odor ligands that activate olfactory receptors that project to specific glomeruli that are involved in generating the odor activity maps.

Proper citation: Olfactory Bulb Odor Map DataBase (OdorMapDB) (RRID:SCR_007287) Copy   

•   Source: SciCrunch Registry

https://github.com/SciCrunch/NIF-Ontology/tree/neurons/ttl

An ontology for describing the complex phenotypes of neurons.

Proper citation: Neuron Phenotype Ontology (RRID:SCR_017403) Copy   

•   Source: SciCrunch Registry

http://nimh-repository.rti.org/

A program that synthesizes, purifies, and distributes otherwise unavailable essential compounds to stimulate basic and clinical research in psychopharmacology relevant to mental health in areas such as the molecular pharmacology and signaling of CNS receptors, longitudinal studies to evaluate the molecular, biochemical, and behavioral actions of psychoactive compounds, and functional brain imaging in both primates and humans. WHAT IS AVAILABLE: * Ligands for CNS receptors, radiolabeled compounds for autoradiography and neuroimaging, biochemical markers, drug analogs and metabolites, and reference standards * Synthesis (including GMP) of promising compounds for mental health research, including preclinical toxicology and safety studies, especially compounds for PET neuroimaging * A listing of currently available NIMH CSDSP compounds is available online at www.nimh-repository.rti.org. RTI International scientists can provide investigators with technical assistance and additional information about the compounds on request. Data sheets containing purity, storage, and handling information are supplied with all NIMH CSDSP compounds. WHO IS ELIGIBLE: Investigators involved in basic or clinical research relevant to mental health are eligible to submit requests. To learn more about current NIMH research areas, please visit the NIMH website at www.nimh.nih.gov. NIMH CSDSP compounds are free to qualified academic investigators, but payment may be required from nonacademic requestors. Investigators interested in obtaining radiolabeled compounds but uncertain about what type of label or specific activity would work best for them may obtain help by communicating with the technical contacts listed on the website.

Proper citation: NIMH Chemical Synthesis and Drug Supply Program (RRID:SCR_004921) Copy   

•   Source: SciCrunch Registry

http://kimlab.io/brain-map/atlas/

Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.

Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) Copy   

•   Source: SciCrunch Registry

https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405

Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.

Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy   

•   Source: SciCrunch Registry

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

Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

Proper citation: VoxBo (RRID:SCR_002166) Copy   

•   Source: SciCrunch Registry

http://gara.bio.uci.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.

Proper citation: Glomerular Activity Response Archive (RRID:SCR_002089) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/DevCCF/

Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain.

Proper citation: 3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) Copy   

•   Source: SciCrunch Registry

https://brainlife.io/docs/using_ezBIDS/

Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms.

Proper citation: ezBIDS (RRID:SCR_025563) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/DevATLAS/

Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome.

Proper citation: DevATLAS (RRID:SCR_025718) Copy   

•   Source: SciCrunch Registry

https://trialweb.dcri.duke.edu/tads/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression.

Proper citation: TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) Copy   

•   Source: SciCrunch Registry

https://resource.loni.usc.edu/resources/atlases/

Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.

Proper citation: International Consortium for Brain Mapping (RRID:SCR_000445) Copy   

•   Source: SciCrunch Registry

http://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

•   Source: SciCrunch Registry