14.9. Sample microscope

This script simulates a microscopic imaging system, generating a random noise image as a mock source and capturing it through a microscope with adjustable magnification, numerical aperture, and wavelength. It visualizes the original and processed images dynamically, demonstrating how changes in optical parameters affect image quality and resolution.

import astropy.units as u
import numpy as np
from openwfs.plot_utilities import grab_and_show, imshow
from openwfs.simulation import Microscope, StaticSource, Camera

specimen_resolution = (1024, 1024)  # height × width in pixels of the specimen image
specimen_pixel_size = 60 * u.nm  # resolution (pixel size) of the specimen image
magnification = 40  # magnification from object plane to camera.
numerical_aperture = 0.85  # numerical aperture of the microscope objective
wavelength = 532.8 * u.nm  # wavelength of the light, for computing diffraction.
camera_resolution = (256, 256)  # number of pixels on the camera
camera_pixel_size = 6.45 * u.um  # Size of the pixels on the camera
p_limit = 100  # Number steps in the animation

# Create a random noise image with a few bright spots
src = StaticSource(
    data=np.maximum(np.random.randint(-10000, 100, specimen_resolution, dtype=np.int16), 0),
    pixel_size=specimen_pixel_size,
)

# Create a microscope with the given parameters
mic = Microscope(
    src,
    magnification=magnification,
    numerical_aperture=numerical_aperture,
    wavelength=wavelength,
)

# simulate shot noise in an 8-bit camera with auto-exposure:
cam = Camera(
    mic,
    analog_max=None,
    shot_noise=True,
    digital_max=255,
)
devices = {"camera": cam, "stage": mic.xy_stage}

if __name__ == "__main__":
    import matplotlib.pyplot as plt

    plt.subplot(1, 2, 1)
    imshow(src.data)
    plt.title("Original image")
    plt.subplot(1, 2, 2)
    plt.title("Scanned image")
    ax = None
    for p in range(p_limit):
        mic.xy_stage.position = p * 1 * u.um
        mic.z_stage.position = p * 0.1 * u.um  # slowly drift out of focus
        ax = grab_and_show(cam, ax)
        plt.title(f"defocus: {mic.z_stage.position}")
        plt.pause(0.2)