exporting-detected-cell-positions-to-brainrender.md

Exporting detected cell positions to brainrender

To convert cell positions (e.g. in cells_in_standard_space.xml) to a format that can be used in brainrender:

Usage

{% hint style="warning" %} This tool is a work in progress, and the usage may change {% endhint %}

    points_to_brainrender cells_in_standard_space.xml exported_cells.h5

Arguments

Run points_to_brainrender -h to see all options.

Positional

• Cellfinder cells file to be converted
• Output filename. Should end with '.h5'. If the containing directory doesn't exist, it will be created.

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 to BrainRender.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()