Clean up Docs

docs/source/add_new_device.rst

@@ -126,7 +126,7 @@ Startup and Configuration
 --------------
 
 Integration with Microscope Object Configurations
-------------------------------------------------
+-------------------------------------------------
 
 -   Each microscope configuration in **navigate** that uses the new device should
     receive a reference to the established communication object.

docs/source/advanced.rst

@@ -158,8 +158,8 @@ hardware.
 **navigate** establishes communication with each device independently, and passes the
 instance of that device to class that controls it (e.g., in this case, the
 `CustomDevice` class). This allows **navigate** to be initialized with multiple
-microscope :ref:`configurations <user_guide/software_configuration:configuration file>`,
-some of which may share devices.
+microscope :ref:`configurations <multiple_microscopes>`, some of which may share devices.
+
 
 .. code-block:: python
 
@@ -470,7 +470,7 @@ Install the plugin using one of two methods:
     * Install a plugin by putting the whole plugin folder directly into
       ``navigate/plugins/``. In this example, put ``custom_device`` folder
       and all its contents into ``navigate/plugins``.
-    * Alernatively, install this plugin through the menu
+    * Alternatively, install this plugin through the menu
       :menuselection:`Plugins --> Install Plugin` by selecting the plugin folder.
 
 The plugin is ready to use. For this plugin, you can now specify a CustomDevice in the

docs/source/conf.py

@@ -89,7 +89,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = ["**/configurations_archive/*", "*archive*", "**/*_archive.rst"]
 
 
 # -- Options for HTML output -------------------------------------------------

docs/source/contributing/contributing_guidelines.rst

@@ -1,3 +1,4 @@
+.. _contributing_guidelines:
 =======================
 Contributing Guidelines
 =======================

docs/source/contributing/feature_container.rst

@@ -14,8 +14,8 @@ Once a feature is executed, any features dependent on this feature's execution
 will execute (for example, move the stage, then snap a picture). Following
 this, the next set of features in sequence will be executed.
 
-Examples of some existing features include ``navigate.model.features.common_features.ZStackAcquisition``, 
-which acquires a z-stack, and ``navigate.model.features.autofocus.Autofocus``, 
+Examples of some existing features include ``navigate.model.features.common_features.ZStackAcquisition``,
+which acquires a z-stack, and ``navigate.model.features.autofocus.Autofocus``,
 which finds the ideal plane of focus of a sample using a discrete cosine transform.
 
 -----------------
@@ -30,7 +30,6 @@ Currently Implemented Features
    ../_autosummary/navigate.model.features.auto_tile_scan
    ../_autosummary/navigate.model.features.autofocus
    ../_autosummary/navigate.model.features.common_features
-   ../_autosummary/navigate.model.features.cva_conpro
    ../_autosummary/navigate.model.features.image_writer
    ../_autosummary/navigate.model.features.remove_empty_tiles
    ../_autosummary/navigate.model.features.restful_features

docs/source/implementations/implementations.rst

@@ -1,3 +1,5 @@
+.. _implemented_microscopes:
+
 ===========================================
 Implemented Microscopes
 ===========================================
@@ -58,10 +60,10 @@ The University of Texas Southwestern Medical Center, Dallas, TX
 **Relevant Publications**:
 
 * `Deconvolution-free subcellular imaging with axially swept light sheet microscopy
-  <https://www.cell.com/biophysj/pdf/S0006-3495(15)00498-1.pdf>`_
+  <https://pubmed.ncbi.nlm.nih.gov/26083920/>`_
 * `Diagonally scanned light-sheet microscopy for fast volumetric imaging of adherent cells
-  <https://www.cell.com/biophysj/pdf/S0006-3495(16)00139-9.pdf>`_
-* `u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions <https://www.cell.com/cell-reports-methods/pdf/S2667-2375(23)00326-0.pdf>`_
+  <https://pubmed.ncbi.nlm.nih.gov/27028654/>`_
+* `u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions <https://pubmed.ncbi.nlm.nih.gov/38042149/>`_
 * `Robust and automated detection of subcellular morphological motifs in 3D microscopy images <https://www.nature.com/articles/s41592-019-0539-z>`_
 
 .. collapse:: Technical Information
@@ -142,7 +144,7 @@ The University of Texas Southwestern Medical Center, Dallas, TX
 **Relevant Publications**:
 
 * `Increasing the field-of-view in oblique plane microscopy via optical tiling
-  <https://opg.optica.org/abstract.cfm?uri=boe-13-11-5616>`_
+  <https://pubmed.ncbi.nlm.nih.gov/36733723/>`_
 * `A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics
   <https://elifesciences.org/articles/57681>`_
 
@@ -215,8 +217,8 @@ The University of Texas Southwestern Medical Center, Dallas, TX
 
 **Relevant Publications**:
 
-* `Adaptive optics in an oblique plane microscope <https://www.biorxiv.org/content/10.1101/2024.03.21.586191v1>`_
-* `Increasing the field-of-view in oblique plane microscopy via optical tiling <https://opg.optica.org/abstract.cfm?uri=boe-13-11-5616>`_
+* `Adaptive optics in an oblique plane microscope <https://pubmed.ncbi.nlm.nih.gov/38562744/>`_
+* `Increasing the field-of-view in oblique plane microscopy via optical tiling <https://pubmed.ncbi.nlm.nih.gov/36733723/>`_
 * `A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics <https://elifesciences.org/articles/57681>`_
 
 .. collapse:: Technical Information
@@ -428,7 +430,7 @@ The University of Texas Southwestern Medical Center, Dallas, TX
 
 **Relevant Publications**:
 
-* `Mechanically sheared Axially Swept Light-Sheet Microscopy <https://www.biorxiv.org/content/10.1101/2024.04.10.588892>`_
+* `Mechanically sheared Axially Swept Light-Sheet Microscopy <https://pubmed.ncbi.nlm.nih.gov/38645073/>`_
 * `The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue <https://www.nature.com/articles/s41592-019-0554-0>`_.
 * `Isotropic imaging across spatial scales with axially swept light-sheet microscopy <https://www.nature.com/articles/s41596-022-00706-6>`_
 * `Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution <https://www.nature.com/articles/s41592-019-0615-4>`_.
@@ -591,8 +593,8 @@ The University of Texas Southwestern Medical Center, Dallas, TX
 
 **Relevant Publications**:
 
-* `Effective elimination of laser interference fringing in fluorescence microscopy by Spinning azimuthal incidence angle <https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20334>`_.
-* `Spinning-spot shadowless TIRF microscopy <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136055>`_
+* `Effective elimination of laser interference fringing in fluorescence microscopy by Spinning azimuthal incidence angle <https://pubmed.ncbi.nlm.nih.gov/16770769/>`_.
+* `Spinning-spot shadowless TIRF microscopy <https://pubmed.ncbi.nlm.nih.gov/26308212/>`_
 
 .. collapse:: Technical Information
 
@@ -824,7 +826,7 @@ Arizona State University, Tempe, AZ
 **Relevant Publications**:
 
 * `Increasing the field-of-view in oblique plane microscopy via optical tiling
-  <https://opg.optica.org/abstract.cfm?uri=boe-13-11-5616>`_
+  <https://pubmed.ncbi.nlm.nih.gov/36733723/>`_
 * `A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics
   <https://elifesciences.org/articles/57681>`_
 

docs/source/index.rst

@@ -79,10 +79,12 @@ technology developers.
    :maxdepth: 1
 
    navigate Plugin Template <https://github.com/TheDeanLab/navigate-plugin-template>
-   navigate Confocal Projection Plugin <https://github.com/TheDeanLab/navigate-confocal-projection>
+   navigate Confocal Projection <https://github.com/TheDeanLab/navigate-confocal-projection>
    navigate at Scale <https://github.com/TheDeanLab/navigate-at-scale>
-   navigate MMCore Plugin <https://github.com/TheDeanLab/navigate-mmcore-plugin>
+   navigate Constant Velocity Acquisition <https://github.com/TheDeanLab/navigate-constant-velocity-acquisition>
+   navigate MMCore <https://github.com/TheDeanLab/navigate-mmcore-plugin>
    navigate ilastik Server <https://github.com/TheDeanLab/navigate-ilastik-server>
+   navigate Photoactivation <https://github.com/TheDeanLab/navigate-photoactivation>
 
 .. toctree::
    :caption: Reference
@@ -96,7 +98,7 @@ technology developers.
 ============
 **navigate** includes key contributions from numerous individuals, both past and
 present, in `The Dean Lab <https://www.dean-lab.org>`_. Please see the accompanying manuscript
-for a full list of contributors. :ref:`Outside contributors <contributing/contributing_guidelines>` are welcome.
+for a full list of contributors. :ref:`Outside contributors  <contributing_guidelines>` are welcome.
 
 **Funding**
 ============

docs/source/plugin/plugin_home.rst

@@ -99,14 +99,14 @@ Plugin Structure:
         │   └── features/
         │           ├── plugin_feature.py
         │           ├── ...
-        │               
+        │
         ├── view/
         |   ├── plugin_name_frame.py
         |   ├── ...
         │
         ├── feature_list.py
         ├── plugin_acquisition_mode.py
-        └── plugin_config.yml 
+        └── plugin_config.yml
 
 
 .. note::
@@ -127,7 +127,7 @@ is:
 
     name: Plugin Name
     view: Popup # or Tab
-    acquisition_modes: 
+    acquisition_modes:
       - name: Plugin Acquisition
         file_name: plugin_acquisition_mode.py
 
@@ -137,8 +137,8 @@ Plugin GUI Elements
 --------------------
 
 **navigate** supports plugins with their own GUIs. A custom plugin GUI can be integrated as a tab or a popup.
-Users should specify a view option in ``plugin_config.yml``. If it is a popup, users can find the plugin under 
-the :guilabel:`Plugins` menu in the **navigate** window. If it is a tab, it will appear next to the 
+Users should specify a view option in ``plugin_config.yml``. If it is a popup, users can find the plugin under
+the :guilabel:`Plugins` menu in the **navigate** window. If it is a tab, it will appear next to the
 :ref:`Settings Notebooks <user_guide/gui_walkthrough:settings notebooks>`.
 
 
@@ -155,7 +155,7 @@ should be named: ``my_plugin_frame.py`` and ``my_plugin_controller.py``.
 Plugin Devices
 ------------------
 
-The **navigate** plugin architecture allows you to integrate new hardware device. There can be more than one 
+The **navigate** plugin architecture allows you to integrate new hardware device. There can be more than one
 device inside a plugin. If they are different kinds of device, please put them into different folders. For each
 kind of device, there should be a ``device_startup_functions.py`` telling **navigate** how to start the device
 and indicating the reference name of the device to be used in ``configuration.yaml``.
@@ -186,16 +186,16 @@ A function to start the device should be given,
         return device_object
 
 
-The template for ``device_startup_functions.py`` can be found in the `plugin template <https://github.com/TheDeanLab/navigate-plugin-template/blob/main/src/plugins-template/model/devices/plugin_device/device_startup_functions.py>`_.
-
+The template for ``device_startup_functions.py`` can be found in the
+`plugin template <https://github.com/TheDeanLab/navigate-plugin-template/blob/main/plugins_template/model/devices/plugin_device/device_startup_functions.py>`_.
 -------------------------------------
 
 Plugin Features
 -------------------------
 **navigate** allows users to add new features. New feature objects and feature lists can each be a plugin or components
 of a plugin. Features and feature lists are automatically loaded into **navigate**.
 
-Please visit `here <https://thedeanlab.github.io/**navigate**/feature_container/feature_container_home.html>`_ for details about how to build a new feature object and feature list.
+Please visit `here <https://thedeanlab.github.io/navigate/contributing/feature_container.html>`_ for details about how to build a new feature object and feature list.
 
 -------------------------------------
 
@@ -204,7 +204,7 @@ Custom Acquisition Modes
 Navigate offers seamless support for custom acquisition modes, and registering a new mode is straightforward.
 
 1. Download the template for `plugin_acquisition_mode.py
-<https://github.com/TheDeanLab/navigate-plugin-template/blob/main/plugins-template/plugin_acquisition_mode.py>`_
+<https://github.com/TheDeanLab/navigate-plugin-template/blob/main/plugins_template/plugin_acquisition_mode.py>`_
 
 2. Update the ``feature_list``.
 
@@ -214,7 +214,7 @@ Navigate offers seamless support for custom acquisition modes, and registering a
     class PluginAcquisitionMode:
         def __init__(self, name):
             self.acquisition_mode = name
-            
+
             self.feature_list = [
                 # update here
             ]
@@ -230,7 +230,7 @@ Users should tell **navigate** what to do before and after acquisition using the
 
     def end_acquisition_controller(self, controller):
         # update here
-    
+
     def prepare_acquisition_model(self, model):
         # update here
 
@@ -241,11 +241,12 @@ Users should tell **navigate** what to do before and after acquisition using the
 
 .. code-block:: none
 
-    acquisition_modes: 
+    acquisition_modes:
         - name: Custom Acquisition
             file_name: plugin_acquisition_mode.py
 
 
 -----------
 
-For more plugin examples, please visit `navigate <https://github.com/TheDeanLab/navigate/tree/develop/src/navigate/plugins>`_ and `Navigate Plugins <https://github.com/TheDeanLab/navigate-plugins>`_.
+For more plugin examples, please visit the plugins in the table of contents menu on
+the left.

docs/source/quick_start.rst

@@ -11,7 +11,7 @@ Installation
 ------------
 
 1. *Install Miniconda.*
-   Download and install Miniconda from the `official website <https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links>`_.
+   Download and install Miniconda from the `official website <https://docs.conda.io/en/latest/miniconda.html>`_.
 
 2. *Create and Activate a Conda Environment.*
    Launch a Miniconda Prompt (or a Terminal on MacOS) and enter the following.
@@ -41,53 +41,52 @@ To save an image to disk, follow these steps:
 
 * Launch **navigate** in synthetic hardware mode as described above.
 
-* Next to the the :guilabel:`Acquire` button on the upper left, make sure that the 
+* Next to the the :guilabel:`Acquire` button on the upper left, make sure that the
   acquisition mode in the dropdown is set to "Continuous Scan".
 
 * Press :guilabel:`Acquire` (:kbd:`ctrl + enter`) and confirm that a synthetic noise image is
   displayed in the :guilabel:`Camera View` window.
 
 .. Note::
-    At least one channel must be selected (checkbox marked) in the 
-    :guilabel:`Channel Settings` window, and all of the parameters (e.g., 
+    At least one channel must be selected (checkbox marked) in the
+    :guilabel:`Channel Settings` window, and all of the parameters (e.g.,
     :guilabel:`Power`) in that row must be populated.
 
-* Select the :guilabel:`Channels` tab. In the :guilabel:`Stack Acquisition Settings` 
+* Select the :guilabel:`Channels` tab. In the :guilabel:`Stack Acquisition Settings`
   window in this tab, press the :guilabel:`Set Start Pos/Foc` button. This specifies
   the starting ``Z`` and ``F`` (e.g., Focus) positions for the stack acquisition.
 
-* Select the :guilabel:`Stage Control` tab (:kbd:`ctrl + 3`), move the ``Z`` stage to 
-  the desired position (e.g., ``100`` μm), go back to the :guilabel:`Channels` tab 
+* Select the :guilabel:`Stage Control` tab (:kbd:`ctrl + 3`), move the ``Z`` stage to
+  the desired position (e.g., ``100`` μm), go back to the :guilabel:`Channels` tab
   (:kbd:`ctrl + 1`), and press the :guilabel:`Set End Pos/Foc` button. This specifies
   the ending ``Z`` and ``F`` positions for the stack acquisition.
 
-* In the :guilabel:`Stack Acquisition Settings` frame, you can now adjust the step 
+* In the :guilabel:`Stack Acquisition Settings` frame, you can now adjust the step
   size, which determines the number of slices in a z-stack.
 
-* In the :guilabel:`Timepoint Settings` window, select :guilabel:`Save Data` 
+* In the :guilabel:`Timepoint Settings` window, select :guilabel:`Save Data`
   by marking the checkbox. If the number of timepoints is set to ``1``, only a single
   stack will be acquired.
 
 * Next to the the :guilabel:`Acquire` button on the upper left, change the acquisition
-  mode in the dropdown to "Z-Stack", and press :guilabel:`Acquire` 
+  mode in the dropdown to "Z-Stack", and press :guilabel:`Acquire`
   (:kbd:`ctrl + enter`).
 
 * A :guilabel:`File Saving Dialog` popup window will appear.
-    * With the exception of :guilabel:`Notes`, all fields must be populated. Any 
+    * With the exception of :guilabel:`Notes`, all fields must be populated. Any
       spaces in the fields will be replaced with an underscore.
-    * :guilabel:`Notes` is saved with the metadata, and can be useful for 
+    * :guilabel:`Notes` is saved with the metadata, and can be useful for
       describing the experiment.
     * :guilabel:`Solvent` is useful for tissue clearing experiments.
-    * :guilabel:`File Type` can be set to :guilabel:`.TIFF`, :guilabel:`OME-TIFF`, 
-      :guilabel:`H5`, or :guilabel:`N5`. The latter two options are pyramidal file 
-      formats that are best used for large datasets and are immediately compatible 
-      with `BigDataViewer <https://imagej.net/plugins/bdv/>`_ and 
+    * :guilabel:`File Type` can be set to :guilabel:`.TIFF`, :guilabel:`OME-TIFF`,
+      :guilabel:`H5`, or :guilabel:`N5`. The latter two options are pyramidal file
+      formats that are best used for large datasets and are immediately compatible
+      with `BigDataViewer <https://imagej.net/plugins/bdv/>`_ and
       `BigStitcher <https://imagej.net/plugins/bigstitcher/index>`_.
     * Press :guilabel:`Acquire` to begin the acquisition.
-    * Once complete, the data can be opened using standard image processing 
+    * Once complete, the data can be opened using standard image processing
       software such as `Fiji <https://imagej.net/software/fiji/>`_.
 
 .. image:: user_guide/images/save_dialog.png
     :align: center
     :alt: File Saving Dialog
-

docs/source/software_installation.rst

@@ -12,10 +12,9 @@ Operating System Compatibility
 
 .. important::
    **navigate** is developed for use on Windows-based systems. This is due to the
-   compatibility of :ref:`device drivers <firmware_overview>` for various microscope
-   hardware components, such as
-   cameras, stages, and data acquisition cards, which are predominantly designed for the
-   Windows environment.
+   compatibility of device drivers for various microscope hardware components, such
+   as cameras, stages, and data acquisition cards, which are predominantly designed
+   for the Windows environment.
 
    While it is possible to launch the software on a Mac using synthetic hardware mode,
    users should be aware of known issues with the Tkinter interface. These issues
@@ -108,7 +107,7 @@ Quick install
 
 **Setup your Python Environment**
 
-Head over to the `miniconda website <https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links>`_
+Head over to the `miniconda website <https://docs.conda.io/en/latest/miniconda.html>`_
 and install the appropriate version based on your operating system.
 
 .. tip::

docs/source/user_guide/case_studies/acquire_exASLM.rst

@@ -22,7 +22,7 @@ unnecessarily results in greater data overhead owing to empty space introduced i
 To avoid this, we also provide a guide on how to perform two axis stage
 scanning which removes the need for computational shearing.
 More information about this microscope and this method, which we refer to as mechanical shearing, can be found
-`here <https://www.biorxiv.org/content/10.1101/2024.04.10.588892v1>`_.
+`here <https://pubmed.ncbi.nlm.nih.gov/38645073/>`_.
 
 .. Constant Velocity Acquisition: