Merge remote-tracking branch 'origin/master'

docs/source/core.rst

@@ -129,13 +129,13 @@ OpenWFS comes with a number of wavefront shaping algorithms already implemented,
 .. list-table::
    :widths: 30 70
 
-   * - :class:`algorithms.FourierDualReference`
+   * - algorithms.FourierDualReference
      - A dual reference algorithm that uses plane waves from a disk in k-space for wavefront shaping :cite:`Mastiani2022`.
-   * - :class:`algorithms.DualReference`
+   * - algorithms.DualReference
      - A generic dual reference algorithm with a configurable basis set :cite:`Cox2024`.
-   * - :class:`algorithms.SimpleGenetic`
+   * - algorithms.SimpleGenetic
      - A simple genetic algorithm for optimiziang wavefronts :cite:`Piestun2012`.
-   * - :class:`algorithms.StepwiseSequential`
+   * - algorithms.StepwiseSequential
      - A simplified version of the original wavefront shaping algorithm :cite:`Vellekoop2007`, with pre-optimization omitted.
 
 All algorithms are designed to be completely hardware-agnostic, so that the exact same code can be used with any type of feedback signal on real or simulated hardware. All algorithms except the :class:`~.SimpleGenetic` algorithm provide support for optimizing multiple targets simulaneously in a single run of the algorithm.

docs/source/micromanager.rst

@@ -5,8 +5,6 @@ OpenWFS in Micro-Manager
 
 To smoothly enable end-user interaction with wavefront shaping algorithms, the Micro-Manager device adapter PyDevice was developed :cite:`PyDevice`. Micro-Manager is a widely-used open-source microscopy control software package. In essence, PyDevice is a Micro-Manager adapter that imports objects from a Python script and integrates them as devices, e.g. a camera or stage. OpenWFS was written in compliance with the templates required for PyDevice, which means OpenWFS cameras, scanners and algorithms can be loaded into Micro-Manager as devices. Examples of this are found in the example gallery :cite:`readthedocsOpenWFS`, and a more detailed description of PyDevice can be found in the mmCoreAndDevices source tree :cite:`mmCoreAndDevices`.
 
-Simulated microscope in Micro-Manager
-----------------------------------------------------
 An example of this integration can be found in :class:`micro_manager_microscope.py`. In this file, a simulated microscope is set up using the tools in  :class:`openwfs.simulation`. In order to expose this to PyDevice, a :class:`dict` object is created named :class:`devices` containing the OpenWFS objects from the simulated microscope. These objects can then be manipulated from Micro-Manager, as seen in figure :numref:`micromanagerconnection`.