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docs/source/readme.rst

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 What is wavefront shaping?
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-Wavefront shaping (WFS) is a technique for controlling the propagation of light in arbitrarily complex structures, including strongly scattering materials :cite:`kubby2019`. In WFS, a spatial light modulator (SLM) is used to shape the phase and/or amplitude of the incident light. With a properly constructed wavefront, light can be made to focus through :cite:`Vellekoop2007`, or inside :cite:`vellekoop2008demixing` scattering materials; or light can be shaped to have other desired properties, such as optimal sensitivity for specific measurements :cite:`bouchet2021maximum`, specialized point-spread functions :cite:`boniface2017transmission`, spectral filtering :cite:`Park2012`,, or for functions like optical trapping :cite:`vcivzmar2010situ`.
+Wavefront shaping (WFS) is a technique for controlling the propagation of light in arbitrarily complex structures, including strongly scattering materials :cite:`kubby2019`. In WFS, a spatial light modulator (SLM) is used to shape the phase and/or amplitude of the incident light. With a properly constructed wavefront, light can be made to focus through :cite:`Vellekoop2007`, or inside :cite:`vellekoop2008demixing` scattering materials; or light can be shaped to have other desired properties, such as optimal sensitivity for specific measurements :cite:`bouchet2021maximum`, specialized point-spread functions :cite:`boniface2017transmission`, spectral filtering :cite:`Park2012`, or for functions like optical trapping :cite:`vcivzmar2010situ`.
 
 It stands out that an important driving force in WFS is the development of new algorithms, for example, to account for sample movement :cite:`valzania2023online`, experimental conditions :cite:`Anderson2016`, to be optimally resilient to noise :cite:`mastiani2021noise`, or to use digital twin models to compute the required correction patterns :cite:`salter2014exploring,ploschner2015seeing,Thendiyammal2020,cox2023model`. Much progress has been made towards developing fast and noise-resilient algorithms, or algorithms designed specifically for the methodology of wavefront shaping, such as using algorithms based on Hadamard patterns or Fourier-based approaches :cite:`Mastiani2022`. Fast techniques that enable wavefront shaping in dynamic samples :cite:`Liu2017,Tzang2019` have also been developed, and many potential applications have been prototyped, including endoscopy :cite:`ploschner2015seeing`, optical trapping :cite:`Cizmar2010`, Raman scattering :cite:`Thompson2016`, and deep-tissue imaging :cite:`Streich2021`. Applications extend beyond that of microscope imaging, such as in optimizing photoelectrochemical absorption :cite:`Liew2016` and tuning random lasers :cite:`Bachelard2014`.
 
@@ -59,9 +59,9 @@ OpenWFS is available on the PyPI repository, and it can be installed with the co
    :language: python
    :caption: ``hello_wfs.py``. Example of a simple wavefront shaping experiment using OpenWFS.
 
-This example uses the `StepwiseSequential` wavefront shaping algorithm :cite:`vellekoop2008phase`. The algorithm needs access to the SLM for controlling the wavefront. This feedback is obtained from a  :class:`~.SingleRoi` object, which takes images from the camera, and averages them over the specified circular region of interest. The algorithm returns the measured transmission matrix in the field `results.t`, which is used to compute the optimal phase pattern to compensate the aberrations. Finally, the code measures the intensity at the detector before and after applying the optimized phase pattern.
+This example uses the `~.StepwiseSequential` wavefront shaping algorithm :cite:`vellekoop2008phase`. The algorithm needs access to the SLM for controlling the wavefront. This feedback is obtained from a  :class:`~.SingleRoi` object, which takes images from the camera, and averages them over the specified circular region of interest. The algorithm returns the measured transmission matrix in the field `results.t`, which is used to compute the optimal phase pattern to compensate the aberrations. Finally, the code measures the intensity at the detector before and after applying the optimized phase pattern.
 
-This code illustrates how OpenWFS separates the concerns of the hardware control (`SLM` and `Camera`), signal processing (`SingleROIProcessor`) and the algorithm itself (`StepwiseSequential`). A large variety of wavefront shaping experiments can be performed by using different types of feedback signals (such as optimizing multiple foci simultaneously using a :class:`~.MultiRoiProcessor` object), using different algorithms, or different image sources, such as a :class:`~.ScanningMicroscope`. Notably, these objects can be replaced by *mock* objects, that simulate the hardware and allow for rapid prototyping and testing of new algorithms without direct access to wavefront shaping hardware (see :numref:`section-simulations`).
+This code illustrates how OpenWFS separates the concerns of the hardware control (:class:`~.SLM` and :class:`~.Camera`), signal processing (:class:`~.SingleRoi(Processor)`) and the algorithm itself (:class:`~.StepwiseSequential`). A large variety of wavefront shaping experiments can be performed by using different types of feedback signals (such as optimizing multiple foci simultaneously using a :class:`~.MultiRoi(Processor)` object), using different algorithms, or different image sources, such as a :class:`~.ScanningMicroscope`. Notably, these objects can be replaced by *mock* objects, that simulate the hardware and allow for rapid prototyping and testing of new algorithms without direct access to wavefront shaping hardware (see :numref:`section-simulations`).
 
 
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