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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.
http://mouse.brain-map.org/static/atlas
Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.
Proper citation: Allen Mouse Brain Reference Atlas (RRID:SCR_002978) Copy
http://www.nitrc.org/projects/quicknii/
Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow.
Proper citation: QuickNII (RRID:SCR_016854) Copy
http://www.nitrc.org/projects/visualign/
Software tool for applying user guided nonlinear refinements (inplane) to existing, affine 2D-to-3D registration. Used for precise quantitative analysis of residual anatomical variability among test subjects after registration with QuickNII. VisuAlign is part of the QUINT workflow.
Proper citation: VisuAlign (RRID:SCR_017978) 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
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
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