Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/cortex-lab/allenCCF
Software tools to work with Allen Inst CCF data in Matlab. MATLAB code to work with the Allen Mouse Brain CCF data.
Proper citation: allenCCF (RRID:SCR_023830) Copy
https://github.com/brainglobe/morphapi
Software Python package for downloading neurons morphological reconstructions from publicly available datasets. With the provided APIs, the user can download data of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization.
Proper citation: MorphAPI (RRID:SCR_023851) Copy
https://github.com/BlueBrain/atlas-splitter
Software tools to split brain atlas regions and refine annotations accordingly. Applicable to the Allen Mouse Brain Atlas
Proper citation: Atlas Splitter (RRID:SCR_023842) Copy
https://github.com/BlueBrain/atlas-direction-vectors
Software tools to compute direction vectors in context of brain atlases.
Proper citation: Atlas Direction Vectors (RRID:SCR_023841) Copy
https://github.com/itsasimiqbal/SeBRe
Software high-throughput Mask R-CNN based toolbox to generate brain atlas through deep learning. Used for segmenting brain regions of interest.
Proper citation: Segmenting Brain Regions (RRID:SCR_023849) Copy
https://quadbio.github.io/VoxHunt/
Software package for assessing brain organoid patterning, developmental state, and cell composition through systematic comparisons of single cell transcriptomes to three-dimensional in situ hybridization data from the Allen Brain Atlas and number of other useful reference datasets.
Proper citation: VoxHunt (RRID:SCR_023829) Copy
https://abagen.readthedocs.io/en/stable/
Software package provides Python interface for aquiring and analyzing Allen Human Brain Atlas microarray expression data.Includes reproducible workflow for processing microarray expression data for further analysis.Used for the Allen Brain Atlas genetics data.
Proper citation: Abagen (RRID:SCR_023832) Copy
https://edspace.american.edu/openbehavior/project/brainrender/
Software Python package for visualizing and interacting with datasets registered to brain atlases. Used for visualization of neuroanatomical and morphological data.
Proper citation: Brainrender (RRID:SCR_022328) Copy
http://genome.ucsc.edu/cgi-bin/hgVisiGene
Virtual microscope for viewing in situ images that show where a gene is used in an organism, sometimes down to cellular resolution. The user can examine cell-by-cell as well as tissue-by-tissue expression patterns. Users can retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. Image set contributions are welcome. The following image collections are currently available for browsing: * High-quality high-resolution images of eight-week-old male mouse sagittal brain slices with reverse-complemented mRNA hybridization probes from the Allen Brain Atlas, courtesy of the Allen Institute for Brain Science * Mouse in situ images from the Jackson Lab Gene Expression Database (GXD) at MGI * Transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology * Mouse head and brain in situ images from NCBI''''s Gene Expression Nervous System Atlas (GENSAT) database * Xenopus laevis in situ images from the National Institute for Basic Biology (NIBB) XDB project
Proper citation: VisiGene Image Browser (RRID:SCR_003341) Copy
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
https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases
Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.
Proper citation: MeshView (RRID:SCR_017222) Copy
https://viewer.cytosplore.org/
Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more.
Proper citation: Cytosplore Viewer (RRID:SCR_018330) 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
Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML
Proper citation: 3DBar (RRID:SCR_008896) Copy
Database of mapped validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text. Operated under the Open Source/Access model, community and scientific networking applications will allow users to store and retrieve their data and to explore cells and their interactions on singular and complex resolution levels. The involvement of stem cell registries and banks will allow direct access to selected cells. The set up the stem cell data repository will involve three lines of action: * the acquisition of scientific data and contents * the standardized description of this data, its organization with the help of ontologies and technical implementation * the integration of existing sources/logistics and to ensure sustainable long-term operation
Proper citation: CellFinder (RRID:SCR_006598) Copy
http://senselab.med.yale.edu/modeldb/
Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.
Proper citation: ModelDB (RRID:SCR_007271) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within NIF that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
