Command Line Interface

neurocollage

Load data from an atlas and a circuit and create a collage figure.

neurocollage [OPTIONS]

Options

--version

Show the version and exit.

-c, --config <config>

Read option defaults from the specified INI file.

--atlas-path <atlas_path>

Required Path to the atlas directory.

--atlas-structure-path <atlas_structure_path>

Required Path to the structure file of the atlas.

--circuit-path <circuit_path>

Required Path to the circuit config file.

--circuit-region <circuit_region>

The region to consider in the circuit.

--circuit-hemisphere <circuit_hemisphere>

The hemisphere to consider in the circuit.

--cells-mtypes <cells_mtypes>

The mtypes to consider in a list.

--cells-sample <cells_sample>

The number of cells that are randomly selected to be plotted.

--cells-ext <cells_ext>

The extension of morphology files.

--planes-count <planes_count>

The number of planes to plot.

--planes-type <planes_type>

The type of planes to plot.

--planes-slice-thickness <planes_slice_thickness>

The thickness of each plane slice.

--planes-centerline-first-bound <planes_centerline_first_bound>

Centerline first bound

--planes-centerline-last-bound <planes_centerline_last_bound>

Centerline last bound

--planes-centerline-axis <planes_centerline_axis>

Centerline axis

--collage-pdf-filename <collage_pdf_filename>

The output file name.

--collage-dpi <collage_dpi>

The DPI used to generate the figure.

--collage-n-pixels <collage_n_pixels>

The number of pixels for plotting layers.

--collage-n-pixels-y <collage_n_pixels_y>

The umber of pixels for plotting y field.

--collage-with-y-field <collage_with_y_field>

Trigger to plot y field.

--collage-with-cells <collage_with_cells>

Trigger to plot the cells.

--collage-plot-neuron-kwargs <collage_plot_neuron_kwargs>

The kwargs passed to the neurom.view.matplotlib_impl.plot_morph function.

--collage-cells-linear-density <collage_cells_linear_density>

Resample the cells to plot less points.

--collage-cells-wire-plot <collage_cells_wire_plot>

Trigger to use matplotlib.pyplot.plot instead of neurom.view.

--random <random>

Randomly sample cells, instead of furthest away choice.

--collage-figsize <collage_figsize>

The size of the output figure.

--collage-nb-jobs <collage_nb_jobs>

The number of parallel jobs to use.

--collage-joblib-verbose <collage_joblib_verbose>

The verbosity of the parallel library.

--3d