The MAP atlas is comprised of a magnetic resonance microscopy (MRM) and an anatomic delineation volume, and a set of software tools for visualization, navigation, and registration of image volumes. The MRM volume is a diffusion-weighted image (DWI) acquired over several hours in a high-field magnet. DWI volumes show a great deal of anatomical detail and good contrast between gray and white matter. Anatomic delineations serve to help orient the user with graphical representations highlighting important anatomical detail and providing a standard description and nomenclature of the region of interest. The anatomical parcellation is based on Brain Maps (Swanson, 1998) with modifications to adapt it to mouse neuroanatomy. The delineations are overlaid upon the MRM volume for visualization.

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The MAP 2D Atlas viewer is a web-based 2D slice viewer that visualizes single slices at a time. An MRI volume, a blockface imaging volume, a nissl-stained volume, and a volume of delineations, are readily accessible, but only a single volume may be viewed at once. This is strictly a slice viewer, orthogonal views are only available when data has also been acquired in orthogonal planes. The user selects a modality and an orientation from the panels on the left. At the bottom of the viewer is a graphical representation of the mouse brain with a bar through it and a thumbnail image. Dragging the bar will scroll through the images, and releasing it will update the main panel on the right with a high-resolution image of the selected slice.