.. _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 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 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:: user_guide/images/save_dialog.png
    :align: center
    :alt: File Saving Dialog