Make a microtubule in napari, for illustration.

microtubule_in_napari.py

import napari
import numpy as np

class MtModel:
    def __init__(
        self, 
        npf: int = 13, 
        start: int = 3, 
        space: float = 4.0, 
        radius: float = 9.8,
    ):
        self.npf = npf
        self.start = start
        self.space = space
        self.radius = radius

    def _make_a_ring(self, offset: int):
        theta = np.linspace(0, 2*np.pi, self.npf, endpoint=False)
        coords = [
            np.linspace(0, self.space*self.start, self.npf, endpoint=False) + self.space*offset,
            self.radius * np.cos(theta),
            self.radius * np.sin(theta),
        ]
        return np.stack(coords, axis=1)

    def polymerize(self, edges: tuple[int, int]) -> np.ndarray:
        start, stop = edges
        tub_a = np.concatenate([self._make_a_ring(offset=2*i) for i in range(start, stop)], axis=0)
        tub_b = np.concatenate([self._make_a_ring(offset=2*i + 1) for i in range(start, stop)], axis=0)
        mt = np.concatenate([tub_a, tub_b], axis=0)
        return mt

    def add_mt(
        self, 
        viewer, 
        edges: tuple[int, int], 
        colors=("magenta", "#f693ff"), 
        name: str = None,
    ):
        mt = self.polymerize(edges)
        n = mt.shape[0] // 2
        face_color = [colors[0]] * n + [colors[1]] * n
        return viewer.add_points(
            mt, face_color=face_color, edge_width=0.1, size=5, name=name
        )

viewer = napari.Viewer()
model = MtModel()
model.add_mt(viewer, (0, 8))