Converting cells to brainrender format¶
Temporary tool until a Cellfinder -> BrainRender bridge is finalised
To convert cell positions (e.g. in cells_in_standard_space.xml
) to
a format that can be used in
BrainRender.
cellfinder_cells_to_brainrender cells_in_standard_space.xml exported_cells.h5
Arguments¶
Run cellfinder_cells_to_brainrender -h
to see all options.
Positional¶
Cellfinder cells file to be converted
Output filename. Should end with ‘.h5’
The following options may also need to be used:¶
-x
or--x-pixel-size
Pixel spacing of the data that the cells are defined in, in the first dimension, specified in um. (Default: 10)-y
or--y-pixel-size
Pixel spacing of the data that the cells are defined in, in the second dimension, specified in um. (Default: 10)-z
or--z-pixel-size
Pixel spacing of the data that the cells are defined in, in the third dimension, specified in um. (Default: 10)--max-z
Maximum z extent of the atlas, specified in um. (Default: 13200)--hdf-key
HDF identifying key. If this has changed, it must be specified in the call toBrainRender.scene.Scene.add_cells_from_file()
To visualise this file in BrainRender¶
from BrainRender.scene import Scene
scene = Scene(jupyter=True)
scene.add_cells_from_file("exported_cells.h5")
scene.render()