feat: init

docs/source/01_getting_started/01_quick_start/01_quick_start.rst

@@ -0,0 +1,60 @@
+.. _Quick_Start_Guide:
+
+=================================
+Quick Start Guide
+=================================
+
+This quick start guide covers how to install **navigate**, launch it in synthetic hardware mode to confirm it is working, and save an image to disk.
+
+Installation
+------------
+
+1. *Install Miniconda.* 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.
+
+   .. code-block:: console
+
+      (base) conda create -n navigate python=3.9.7
+      (base) conda activate navigate
+
+3. *Install* **navigate**.
+
+   .. code-block:: console
+
+      (navigate) pip install navigate-micro
+
+4. *Launch* **navigate** *in synthetic hardware mode.* This will allow you to test its functionality without actual hardware.
+
+   .. code-block:: console
+
+      (navigate) navigate -sh
+
+Saving a Z-Stack to Disk
+------------------------
+
+To save an image to disk, follow these steps:
+
+* Launch **navigate** in synthetic hardware mode as described above.
+* Next to 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., :guilabel:`Power`) in that row must be populated.
+
+* 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 (: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 size, which determines the number of slices in a z-stack.
+* 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 :guilabel:`Acquire` button on the upper left, change the acquisition 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 spaces in the fields will be replaced with an underscore.
+    * :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 `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 software such as `Fiji <https://imagej.net/software/fiji/>`_.
+
+.. image:: images/save_dialog.png
+    :align: center
+    :alt: File Saving Dialog