save_secondary_reference#

brainglobe_atlasapi.atlas_generation.stacks.save_secondary_reference(stack, name, output_dir)[source]#

Save a secondary reference image stack with a given name.

Ensures the stack is of the correct data type before saving.

Parameters:

  • stack (np.ndarray) – The secondary reference image stack.

  • name (str) – The base name for the output file (e.g., “my_secondary_reference”).

  • output_dir (Path) – The directory where the secondary reference image will be saved.