Image space definition

In some BrainGlobe tools, you need to specify the orientation and resolution of the data.

Orientation

When you need to specify the orientation of your data, you will usually need to enter a string in the brainglobe-space “initials” form, to describe the origin voxel.

When you work with a stack, the origin is the upper left corner when you show the first element stack[0, :, :] with matplotlib or when you open the stack with ImageJ. The first dimension is the one that you are slicing, the second is the height of the image, and the third is the width of the image.

If the origin of your data (first, top left voxel) is the most anterior, superior, left part of the brain, then the orientation string would be “asl” (anterior, superior, left), and you would use asr.

The order of the three initials must be the same as the axis order (sliced plane, height, width).

For help with setting the orientation, the brainreg napari plugin comes with a tool to interactively check the orientation (see documentation).

Examples

Coronal section

If the first plane of this image was olfactory bulb, it would be asr (or asl). If the first plane was cerebellum, it would be psr or psl.

Horizontal section

If the first plane of this image was the top of the brain it would be sal/sar. If the first plane was the base it would be ial/iar.

Voxel sizes

You may also need to specify the size of your voxels. These voxel sizes are in microns, and come in the same order as your orientation definition.

As an example, we will assume, as above, the origin of your data (first, top left voxel) is the most anterior, superior, left part of the brain. If your plane spacing (i.e., the z-depth is 5 microns), and your in-plane resolution is 2x2 microns, then the voxel sizes would be 5 2 2.