New feature: percentage of neuronal mass with respect to soma

[lidakanari]

We need a feature to measure the percentage of mass "above" and "below" the soma. The direction is determined based on the selected axis (default='Y').

A draft for this feature can be found here:

from neurom.core.morphology import iter_neurites
from neurom.core.types import tree_type_checker as is_type
from neurom.features import section as sf


def get_mass_above_soma(neuron, neurite_type, axis='Y'):
    """Computes the percentage of points above / below the soma
       with respect to the selected axis.
    """
    col = getattr(neurom.COLS, axis)

    points = list(
            iter_neurites(neuron, mapfun=sf.section_points, filt=is_type(neurite_type))
        )
    point_sel = np.vstack(points)[:, col]
    soma_center = neuron.soma.center
    return 100 * np.count_nonzero(point_sel > soma_center[col]) / len(point_sel)

Example values for a test neuron

neuron = neurom.load_morphology('./tests/data/neurolucida/bio_neuron-000.asc')

get_mass_above_soma(neuron, neurite_type=neurom.AXON, axis='Y') == 73.25581395348837
get_mass_above_soma(neuron, neurite_type=neurom.AXON, axis='X') == 56.60377358490566
get_mass_above_soma(neuron, neurite_type=neurom.AXON, axis='Z') == 26.39315489249671

get_mass_above_soma(neuron, neurite_type=neurom.BASAL_DENDRITE, axis='Z') == 48.285198555956676
get_mass_above_soma(neuron, neurite_type=neurom.BASAL_DENDRITE, axis='X') == 50.90252707581227
get_mass_above_soma(neuron, neurite_type=neurom.BASAL_DENDRITE, axis='Y') == 62.99638989169675

[adrien-berchet]

If you want to estimate the mass, shouldn't you sum up the lengths (volumes would be even better) of the segments above or below the soma? The number of points is a good approximation only if the morphology was resampled before calling this function.

[lidakanari]

Yes, you are right @adrien-berchet, computing the length percentages would actually be better. @eleftherioszisis can you easily implement this with lengths?

[lidakanari]

One more comment, I'm not sure if this should be 100% maybe just leave the value without the 100. Thanks!