.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/micro_manager_microscope.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_micro_manager_microscope.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_micro_manager_microscope.py:

Micro-Manager simulated microscope
======================================================================
This script simulates a microscope with a random noise image as a mock specimen.
The numerical aperture, stage position, and other parameters can be modified through the Micro-Manager GUI.

To use it:
  * make sure  you have the PyDevice adapter installed in Micro-Manager (install the nightly build if you don't have it).
  * load the micro_manager_microscope.cfg hardware configuration in Micro-Manager,
  * locate the micro_manager_microscope.py in the file open dialog box that popps up.
  * take a snapshot or turn on live preview, you may need to auto-adjust the color scale
  * experiment with the numerical aperture or set the stage X and Y position in the device properties.

See the 'Sample Microscope' example for a microscope simulation that runs from Python directly.

.. GENERATED FROM PYTHON SOURCE LINES 15-53

.. code-block:: Python


    import astropy.units as u
    import numpy as np

    from openwfs.simulation import Microscope, StaticSource, Camera, SLM
    from openwfs.utilities.patterns import gaussian

    specimen_resolution = (512, 512)  # height × width in pixels of the specimen image
    specimen_pixel_size = 120 * 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

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

    slm = SLM(shape=(100, 100), field_amplitude=gaussian((100, 100), waist=1.0))

    # Create a microscope with the given parameters
    mic = Microscope(
        source=src,
        magnification=magnification,
        numerical_aperture=numerical_aperture,
        wavelength=wavelength,
        incident_field=slm.field,
    )

    # simulate shot noise in an 8-bit camera with auto-exposure:
    cam = Camera(mic, analog_max=None, shot_noise=True, digital_max=255)

    # construct dictionary of objects to expose to Micro-Manager
    devices = {"camera": cam, "stage": mic.xy_stage}


.. _sphx_glr_download_auto_examples_micro_manager_microscope.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: micro_manager_microscope.ipynb <micro_manager_microscope.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: micro_manager_microscope.py <micro_manager_microscope.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: micro_manager_microscope.zip <micro_manager_microscope.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_