diff --git a/docs/source/core.rst b/docs/source/core.rst index 407f6d3..be5488c 100644 --- a/docs/source/core.rst +++ b/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. diff --git a/docs/source/micromanager.rst b/docs/source/micromanager.rst index e4190e8..7512945 100644 --- a/docs/source/micromanager.rst +++ b/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`.