Image space definition#
In some BrainGlobe tools, you need to specify the orientation and resolution of the data.
Orientation#
To describe the orientation of 3D brain imaging data in anatomical terms, brainglobe-space uses a anatomical description of the relative location of the origin—the voxel at position [0, 0, 0], which when you open the stack with napari by default corresponds with the pixel in the upper left corner of the first image in the stack.
The origin can be described by a three letter string in which each letter corresponds to one of the following anatomical directions:
posterior (
p) ↔ anterior (a)superior (
s) ↔ inferior (i)left (
l) ↔ right (r)
The string includes one letter from each opposing pair, specifying the direction towards the origin for axes 0, 1, and 2 respectively.
50 μm mouse brain atlas by Wang et al., 2020, visualised in napari using the brainrender-napari plugin.
Examples#
The examples below assume default ordering of the axes, i.e. axis 0 (slice depth), axis 1 (image height), axis 2 (image width).
Coronal#
If the stack of images starts at the olfactory bulb, moving toward the cerebellum, the anatomical directions for each axis are:
Axis 0: anterior → posterior
Axis 1: superior → inferior
Axis 2: left → right
The origin voxel corresponds to the most anterior (a), superior (s), left (l) part of the brain, so the origin string is asl.
If the stack would start at the cerebellum and move towards the olfactory bulb, then axis 0 runs posterior → anterior, and the origin string would be psl.
Horizontal#
If the first image in the stack corresponds to the bottom of the brain, the origin voxel corresponds to the most inferior (i), anterior (a), left (l) part of the brain for axis 0, 1, and 2 respectively. In this case the origin string is ial.
Sagittal#
If the stack is sliced from the left side of the brain toward the right, the origin corresponds to the most left (l), superior (s), anterior (a) part of the brain, so the origin string is lsa.
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 slice depth) is 5 microns, and your in-plane resolution is 2x2
microns, then the voxel sizes would be 5 2 2.
Napari 3D Orientation for brainrender#
napari v0.6.0 and later use a right-handed 3D coordinate system by default, however brainrender expects a left-handed system, so 3D visualisations may appear mirrored (left-right flipped).
To change to a left-handed system
Right-click the Toggle 2D/3D view button in the bottom-left corner.
Select the pre-0.6.0 default: away, down, right.
This ensures napari’s visualisation matches brainrender’s.
For more details on napari’s 3D axis directions and handedness, see the napari documentation.