- Neuron Atlas is a tool to visualize the spatial distribution of the rodent neurons available in NeuroMorpho.Org, based on and adapted from the Brain Explorer application of the Allen Brain Institute.
- Each sphere in Neuron Atlas represents a single rodent reconstruction from NeuroMorpho.Org. The sphere is placed randomly within the appropriate regionfor the corresponding neuron, as mapped onto the Allen Reference Atlas. Hence the mapping between the atlas and the database is only informative at the regional level. Principal neurons, Non-pyramidal principal neurons, and Interneurons are each represented by a distinct color.
- Hovering the pointer over a sphere displays the reconstruction details, including its cell type, name in NeuroMorpho.Org, and the archive to which it belongs. The highlighted sphere turns green until a subsequent sphere is hovered over. Left-clicking a sphere displays the corresponding reconstruction in a separate 3D Neuron Viewer. Right-clicking a sphere calls the NeuroMorpho.Org reconstruction page.
- The brain structures can be viewed by selecting the "Show Searchable Structures" under the Atlas drop-down option on the file menu. The brain regions for which rodent reconstructions are available in NeuroMorpho.Org are listed in the right panel display under the "[A]reas and [N]eurons" tab. Specific structures can be toggled using the A selections and the neurons present in specific regions can be toggled using the N selections.
- The "Saved Views" in this same panel contains saved rotations of the visualization.
The visualization of the brain can be rotated by holding the right-click of the mouse and can moved across the plane by holding the left-click of the mouse. Left-clicking on the Atlas zooms into the visualization and right-clicking zooms out.
- Sagittal, horizontal, and coronal sections can be selected (three icons on toolbar or in the drop-down menu) and superimposed for additional visualization options. These sections can be panned by holding on right-click button of the mouse. The images for these sections are extracted from the Allen Brain Atlas.
NOTE: For MAC laptops - Use the shift key with the trackpad to emulate a right click.
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