test_brain
with 270 .tif
imagestest_brain
directory)brainreg_output
in the same directory as the test_brain
)psl
, which means that the data origin is the most posterior, superior, left voxel. For more details see Image definition​brainglobe list
. In this case, we want to use a mouse atlas (as that's what our data is), and we'll use the 50um version of the Allen Mouse Brain Atlas. test_brain
directory into the main napari window. Then load the plugin by selecting brainreg-register: Atlas registration
from the napari Plugins
menu. Image layer
- Set this to the test_brain
image layerAtlas
- Set this to allen_mouse_50um
Data orientation
- Set this to psl
Voxel size (z)
- Set to 50Voxel size (x)
- Set to 40Voxel size (y)
- Set to 40Output directory
- Click Choose directory
, and create a new directory in the same directory as test_brain
called brainreg_output
Run
, and the registration will start. Lots of stuff will get printed to the console as brainreg runs, and when it's done (it should only take a minute or so), you will see something like: