<jupyter_start><jupyter_text>Load data, create atlas object<jupyter_code># where to look for the dataset
dset_dir = '../../data/processed/starling/'
# create the atlas
starling_atlas = atlas(
    species = 'starling',
    dset_dir = dset_dir,
    um_mult = 100,
    smoothing = ['Brain', 'Brainregions', 'Nuclei']
)<jupyter_output>qform_code 32 not valid; setting to 0
qform_code 32 not valid; setting to 0
qform_code 32 not valid; setting to 0
qform_code 32 not valid; setting to 0<jupyter_text>Plot brain regions<jupyter_code>plot_transection(starling_atlas, regions_to_plot='Brainregions', n_slice = 8);<jupyter_output><empty_output><jupyter_text>Plot nuclei<jupyter_code>plot_transection(starling_atlas, regions_to_plot='Nuclei', region_alpha = 0.5);<jupyter_output><empty_output>
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