Update from develop

Author: AdvancedImagingUTSW

README.md

@@ -11,7 +11,8 @@ navigate
 [![Tests](https://github.com/TheDeanLab/navigate/actions/workflows/push_checks.yaml/badge.svg)](https://github.com/TheDeanLab/navigate/actions/workflows/push_checks.yaml)
 [![codecov](https://codecov.io/gh/TheDeanLab/navigate/branch/develop/graph/badge.svg?token=270RFSZGG5)](https://codecov.io/gh/TheDeanLab/navigate)
 
-Navigate is an open source Python package for control of light-sheet microscopes. It allows for easily reconfigurable hardware setups and automated acquisition rotuines.
+**navigate** is an open source Python package for control of light-sheet microscopes.
+It allows for easily reconfigurable hardware setups and automated acquisition rotuines.
 
 ### Quick install
 
@@ -31,23 +32,27 @@ Please refer to and contribute to the documentation, which can be found on GitHu
 
 ### Command Line Arguments
 
-* optional arguments:
-	*  -h, --help            show this help message and exit
-
-* Input Arguments:
-  	* -sh, --synthetic_hardware
-  	* --config_file CONFIG_FILE
-  	* --experiment_file EXPERIMENT_FILE
-  	* --etl_const_file ETL_CONST_FILE
-	*  --rest_api_file REST_API_FILE
-  	* --logging_config LOGGING_CONFIG
-
-### Authors
-* Kevin Dean
-* Zach Marin
-* Xiaoding 'Annie' Wang
-* Dax Collison
-* Sampath Rapuri
-* Samir Mamtani
-* Renil Gupta
-* Andrew Jamieson
+Below are the optional arguments that can be passed to the navigate software:
+
+- `-h, --help`
+  Provides information on the optional arguments that can be passed to **navigate**.
+- `-sh, --synthetic_hardware`
+  Open the software without any hardware attached for testing
+  and setting up a new system.
+- `-c, --configurator`
+  Open the **navigate** configuration wizard, which provides a
+  graphical interface for setting up the hardware configuration.
+- `-d`
+  Enables the debugging menu in the software.
+- `--config-file`
+  Pass a non-default `configuration.yaml` file to **navigate**.
+- `--experiment_file`
+  Pass a non-default `experiment.yaml` file to **navigate**.
+- `--gui-config-file`
+  Pass a non-default `gui_config.yaml` file to **navigate**.
+- `--waveform-constants-file`
+  Pass a non-default waveform constants file to **navigate**.
+- `--rest_api_file`
+  Pass a non-default REST API file to **navigate**.
+- `--logging_config`
+  Pass a non-default logging configuration file to **navigate**.

docs/source/user_guide/case_studies/acquire_exASLM.rst

@@ -12,9 +12,11 @@ To achieve this, **navigate** receives a `trigger signal <http://www.asiimaging.
 from the stage controller to start image acquisition once
 the stage has reached the desired position and velocity. Thereafter, **navigate** acquires images
 at a constant rate until the stage has reached the end position. This mode of acquisition is termed
-"Constant Velocity Acquisition", and is implemented as a feature in **navigate**.
+"Constant Velocity Acquisition", and is implemented as a plugin in **navigate**. To
+download the plugin, please visit `navigate-constant-velocity-acquisition
+<https://github.com/TheDeanLab/navigate-constant-velocity-acquisition>`_.
 
-Furthermore, since the stage moves at a 45 degree angle relative to the microscope detection axis,
+Since the stage moves at a 45 degree angle relative to the microscope detection axis,
 computational shearing of the data is necessary. For large data sets, this can become computationally challenging and
 unnecessarily results in greater data overhead owing to empty space introduced in the data.
 To avoid this, we also provide a guide on how to perform two axis stage

docs/source/user_guide/file_formats.rst

@@ -58,7 +58,7 @@ Image Writing Benchmarks
 ------------------------
 
 To evaluate the performance of saving imaging data in different formats, we conducted
-benchmarks on a RedHat Linux system. We assessed the median disk write time for TIFF,
+benchmarks on a Windows 10 system. We assessed the median disk write time for TIFF,
 OME-TIFF, H5, N5, and OME-Zarr formats across image resolutions of 512x512,
 1024x1024, and 2048x2048 under two conditions: (A) capturing 1000 single-plane
 images and (B) acquiring a single z-stack composed of 1000 planes. All times

docs/source/user_guide/hardware/configurations/configuration_mesospimbt.yaml

@@ -1,4 +1,3 @@
-# Only one microscope can be active in the GUI at a time, but all microscopes will be accessible
 microscopes:
   BTMesoSPIM:
     daq:
@@ -45,7 +44,7 @@ microscopes:
     filter_wheel:
       hardware:
         type: ASI #SyntheticFilterWheel #SutterFilterWheel
-        wheel_number: 1
+        wheel_number: 0
         port: COM8
         baudrate: 115200
       filter_wheel_delay: .030 # in seconds