unravel.allen_institute.abca.merfish.merfish_slice module#

Use abca_merfish_slice or mf_slice from UNRAVEL to plot a MERFISH slice from the Allen Brain Cell Atlas (ABCA).

Note

https://alleninstitute.github.io/abc_atlas_access/notebooks/merfish_ccf_registration_tutorial.html#read-in-section-reconstructed-and-ccf-coordinates-for-all-cells
The slice index ranges from 05 to 67.
Missing slices include: 07 20 21 22 23 34 41 63 65.

Usage for color mode (choose cell_metadata.csv color column):#

abca_merfish_slice -b path/to/base_dir -s 40 -c subclass_color -o slice40_subclass.png

Usage for gene expression mode:#

abca_merfish_slice -b path/to/base_dir -s 40 -g Htr2a –imputed -o slice40_Htr2a_imputed.png

Usage for overlaying neurons:#

abca_merfish_slice -b path/to/base_dir -s 40 -g Htr2a –neurons -o slice40_Htr2a_neurons.png

unravel.allen_institute.abca.merfish.merfish_slice.parse_args()[source]#

unravel.allen_institute.abca.merfish.merfish_slice.join_cell_metadata(csv_path, base, neurons_only=False)[source]#: Return a fully-joined cell metadata DataFrame.

unravel.allen_institute.abca.merfish.merfish_slice.legend_prep(ax, df_section, color_col, legend_loc)[source]#

Build a categorical legend using the label column associated with <color_col>.

Parameters:

color_col (str) –
legend_loc (str) –

unravel.allen_institute.abca.merfish.merfish_slice.main()[source]#