Format of Template Directory

[nickeener]

Hi, first thanks for creating this useful tool! I was trying to use the build_probability_map and simulate_localization_pattern functions in order to create simulated cells with specific transcript localization patterns but am a bit confused as to how the template directory that they use as input should be formatted as this does not appear to be described at all in the documentation. From this chunk of code of utils.py (lines 244 - 256) from the build_template function:

    # read files
    path = os.path.join(
        path_template_directory, "cell_mask_{0}.npy".format(filename))
    coord_cell_mask = stack.read_array(path)
    path = os.path.join(
        path_template_directory, "cell_map_{0}.npy".format(filename))
    coord_cell_map = stack.read_array(path)
    path = os.path.join(
        path_template_directory, "nuc_mask_{0}.npy".format(filename))
    coord_nuc_mask = stack.read_array(path)
    path = os.path.join(
        path_template_directory, "nuc_map_{0}.npy".format(filename))
    coord_nuc_map = stack.read_array(path)

It seems like it needs four files: cell_mask_{filename}.npy, cell_map_{filename}.npy, nuc_mask_{filename}.npy, and nuc_map_{filename}.npy where filename = "{i_cell}_{shape_str}_{protrusion_flag}". but what exactly these files are is unclear to me. Are they binary image masks files or lists of points? And what is the difference between the mask and map files?

Apologies if this is stated somewhere in the documentation.