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Welcome to Atlas3D

What is Atlas3D?
Atlas3D is a multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data.

Are there any atlases available with the tool?
  • 32 mouse brain structures 3-D reconstructed from “The Mouse Brain in Stereotaxic Coordinates” by Paxinos & Franklin (2001)
    Link to the publisher
  • 62 rat brain structures 3-D reconstructed from  “The Rat Brain in Stereotaxic Coordinates” by Paxinos & Watson (2005)
    Link to the publisher

What kind of features does the tool provide?
The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework.

What data formats can be imported into Atlas3D?
Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative, http://nifti.nimh.nih.gov) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported.

How can the Atlas3D tool be used in image analysis?  
Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

The Atlas3D project is directed by Jan G. Bjaalie, Neural Systems and Graphics Computing Laboratory, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1105 Blindern, N-0317 Oslo, Norway.

Webmaster and Atlas3D development: Dmitri Darine

Atlas3D reference
Neural Systems and Graphics Computing Laboratory www.NeSys.uio.no