reordered sections, editing documentation

docs/source/conclusion.rst

@@ -5,7 +5,7 @@ In this work we presented an open-source Python package for conducting and simul
 
 OpenWFS incorporates features to reduce the chances of errors in the design of wavefront shaping code. Notably, the use of units of measure prevents the accidental mixing of units, and the automatic synchronization mechanism ensures that hardware is properly synchronized without the need to write any synchronization code. Finally, the ability to simulate full experiments, and to mock individual components, allows the user to test wavefront shaping algorithms without the need for physical hardware. We find this feature particularly useful since there is a lot that can go wrong in an experiment, (also see :cite:`Mastiani2024PracticalConsiderations`), and experimental issues and software issues are not always easy to distinguish. With OpenWFS, it is now possible to fully test the algorithms before entering the lab, which can save a lot of time and frustration.
 
-We envision that OpenWFS will hold a growing collection of components for hardware control, advanced simulations, and wavefront shaping. The standardised interfaces for detectors, actuators and SLMs, enables the cooperative development of complex functionality. Additionally, standardized components and algorithms will greatly simplify developing reusable code that can be used across different setups and experiments. The simulation tools may additionally be used for research and education, ushering in a new phase of applications in wavefront shaping. We therefore encourage the reader to join us in developing new algorithms and components for this framework.
+We envision that OpenWFS will hold a growing collection of components for hardware control, advanced simulations, and wavefront shaping. Further expansion of the supported hardware is of high priority, especially wrapping c-based libraries and adding support for  Micro-Manager device adapters. The standardised interfaces for detectors, actuators and SLMs will greatly simplify developing reusable code that can be used across different setups and experiments. The simulation tools may additionally be used for research and education, ushering in a new phase of applications in wavefront shaping. We therefore encourage the reader to join us in developing new algorithms and components for this framework.
 
 Code availability
 ------------------------------------------------

docs/source/conf.py

@@ -43,6 +43,8 @@
 latex_elements = {
     "preamble": r"""
         \usepackage{authblk}
+        \usepackage{etoolbox}        % Reduce font size for all tables
+        \AtBeginEnvironment{tabular}{\small}
      """,
     "maketitle": r"""
         \author[1]{Daniël~W.~S.~Cox}
@@ -61,16 +63,21 @@
                 this research field is expanding rapidly. 
                 As the field advances, it stands out that many breakthroughs are driven by the development of better 
                 software that incorporates increasingly advanced physical models and algorithms.
-                Typical control software involves fragmented implementations for scanning microscopy, image processing, 
-                optimization algorithms, low-level hardware control, calibration and troubleshooting, 
-                and simulations for testing new algorithms. 
-
-                The complexity of the many different aspects of wavefront shaping software, however, 
-                is becoming a limiting factor for further developments in the field, as well as for end-user adoption.
-                OpenWFS addresses these challenges by providing a modular and extensible Python library that 
-                incorporates elements for hardware control, software simulation, and automated troubleshooting. 
-                Using these elements, the actual wavefront shaping algorithm and its automated tests can be written
-                in just a few lines of code.
+                
+                Typical WFS software involves a complex combination of low-level hardware control, signal processing, 
+                calibration, troubleshooting, simulation, and the wavefront shaping algorithm itself.
+                This complexity makes it hard to compare different algorithms and to extend existing software with new
+                hardware or algorithms. Moreover, the complexity of the software can be a significant barrier for end
+                users of microscopes to adopt wavefront shaping.
+
+                OpenWFS addresses these challenges by providing a modular Python library that 
+                separates hardware control from the wavefront shaping algorithm itself. 
+                Using these elements, an wavefront shaping algorithm can be written
+                in just a few lines of code, with OpenWFS taking care of low-level hardware control, synchronization,
+                and troubleshooting. Algorithms can be used on different hardware or in a completely
+                simulated environment without changing the code. Moreover, we provide full integration with
+                the \textmu Manager microscope control software, enabling wavefront shaping experiments to be
+                executed from a user-friendly graphical user interface. 
             }
         }
         \maketitle

docs/source/index.rst

@@ -9,7 +9,8 @@ OpenWFS - a library for conducting and simulating wavefront shaping experiments
     core
     slms
     simulations
+    micromanager
+    troubleshooting
     development
-    pydevice
     api
     auto_examples/index

docs/source/index_latex.rst

@@ -9,8 +9,7 @@ OpenWFS - a library for conducting and simulating wavefront shaping experiments
     core
     slms
     simulations
-    pydevice
+    micromanager
+    troubleshooting
     development
     conclusion
-
-    auto_examples/index

docs/source/pydevice.rst → docs/source/micromanager.rst

@@ -1,6 +1,6 @@
-.. _section-pydevice:
+.. _micromanager:
 
-OpenWFS in PyDevice
+OpenWFS in μ-Manager
 ==============================================
 
 To smoothly enable end-user interaction with wavefront shaping algorithms, the Micro-Manager device adapter PyDevice was developed :cite:`PyDevice`. A more detailed description can be found in the mmCoreAndDevices source tree :cite:`mmCoreAndDevices`. In essence, PyDevice is 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`. Further developments due to this seamless connection can be a dedicated Micro-Manager based wavefront shaping GUI.