Clean up Docs

`sphinx-build -b linkcheck . _build/linkcheck` used to check all links, many of which were broken. Needs to be launched from the same directory that the `conf.py` file is in.

Author: AdvancedImagingUTSW

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::