feat: init

docs/source/04_faq/issues/01_channel_switching.rst

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+Slow Channel Switching
+----------------------
+
+When we operate multiple channels, there is a clear time delay between channels. This is most obvious when operating in the continuous mode, or when you are acquiring a Z-stack in the Per Z Laser Cycling mode.
+
+This delay is associated with the time it takes to load the waveforms onto the DAQ card. One possible solution is to write the waveforms to different channels on the DAQ, but this would require that the analog/digital signals be combined physically. For example, if CH00 was delivered on AO0, and CH01 was delivered on AO1, but both were communicating with a single laser, then the signals could be combined and delivered to the laser. However, a more obvious solution would be to reduce the time necessary to load the waveforms onto the DAQ card. One immediate way to do this is by reducing the DAQ sampling rate, but this would reduce the resolution of the waveforms. More sophisticated DAQ systems, including an FPGA, could also be used to eliminate this delay.

docs/source/04_faq/issues/02_histogram.rst

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+
+Histogram Lag in GUI
+---------------------
+
+A known issue in the current version is that the histogram display can introduce noticeable lag in the graphical user interface, especially during high-speed imaging or when using a camera with a very large number of pixels. We are actively evaluating alternative strategies to improve performance. In the meantime, users can disable the histogram to improve responsiveness by right-clicking on it and selecting the appropriate entry from the popup menu. The histogram can be re-enabled the same way.

docs/source/04_faq/issues/issues_home.rst

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+============
+Known Issues
+============
+
+This page lists known issues with the **navigate** software that currently do not have an obvious solution. Please report any other issues you encounter on GitHub.
+
+.. _issues-home:
+
+In this section, we outline some common challenges encountered in setting up a microscope system and provide solutions to address these issues effectively.
+
+.. toctree::
+   :maxdepth: 1
+
+   01_channel_switching
+   02_histogram
+
+
+
+
+

docs/source/04_faq/troubleshooting/01_proxy.rst

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+Proxy Configuration
+===================
+
+Overview
+--------
+If the software is run at an institution with a proxy, you may need to update your proxy settings to allow ``pip`` and ``conda`` to install the proper packages.
+
+Solution and Verification
+-------------------------
+
+* Setting up your proxy can be done by going to Environment Variables for Windows, or another OS equivalent.
+* Create the following new System Variables (please see that they are both http, this is purposeful and not a typo):
+
+    * Variable = HTTP_PROXY; Value = http://proxy.your_university.edu:1234
+    * Variable = HTTPS_PROXY; Value = http://proxy.your_university.edu:1234
+
+* If you continue to have issues then change the value of Variable HTTPS_PROXY to https://proxy.your_university.edu:1234
+
+* If you still have issues then you will need to create/update both configuration files for conda and pip to include proxy settings, if they are not in the paths below you will need to create them. This assumes a Windows perspective. Mac/Linux users will have different paths, they can be found online.
+
+    * The ``conda`` configuration file can be found at C:\\Users\\UserProfile\\.condarc
+    * The ``pip`` configuration file can be found at C:\\Users\\UserProfile\\pip\\pip.ini
+
+* You can also try to set the proxy from within the Anaconda Prompt:
+*  ``set https_proxy=http://username:password@proxy.example.com:8080``
+*  ``set http_proxy=http://username:password@proxy.example.com:8080``

docs/source/04_faq/troubleshooting/02_usb_connectivity.rst

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+
+.. _obis_tiger_connection:
+
+Intermittent USB Connectivity
+===============================
+
+Overview
+--------
+For setups that include **Coherent OBIS lasers** and an **ASI Tiger Controller**, some users have reported intermittent connection issues. These errors were first observed at CU Boulder, where the Coherent OBIS laser and the ASI Tiger controller appeared to experience conflicts over COM port assignments.
+
+Reported Issues
+---------------
+1. **Connection Failure with the ASI Stage**:
+
+   - The ASI stage intermittently fails to connect, with an error message reading: "Unable to connect to the serial port: Access to the port ‘COM13’ is denied."
+   - This error has occurred in both the Tiger control software and *navigate*.
+
+2. **Error Logs in Navigate**:
+
+   - In the navigate software, the error is logged as: `"model - ERROR - asi: ASI stage connection failed"`.
+
+3. **Stage Malfunction During Imaging**:
+
+   - When a connection was achieved, the ASI stages exhibited sporadic movements during image acquisition.
+
+Suspected Cause
+---------------
+Upon investigation, the issue appeared to stem from **port competition** between the Coherent OBIS laser and the ASI Tiger controller. In this setup:
+
+   - The ASI Tiger controller was assigned to **COM port 13**.
+   - The Coherent OBIS 561 nm laser was initially assigned to **COM port 14**.
+
+Despite this configuration, the Coherent OBIS laser intermittently attempted to connect through COM port 13, effectively displacing the ASI Tiger controller's access to the port and causing a conflict.
+
+Solution and Verification
+-------------------------
+To address this issue, the following corrective actions were implemented:
+
+1. **Reassigning the Coherent OBIS Laser**:
+
+   - The Coherent OBIS laser was reassigned from COM port 14 to **COM port 9** to prevent interference with the ASI Tiger controller. This port was chosen since it was in close proximity to the other Coherent OBIS laser instances.
+
+2. **System Reboot**:
+
+    - Following the reassignment, both the computer and hardware were rebooted to ensure the new COM port configurations took effect.
+
+Results
+-------
+Since reassigning the Coherent OBIS laser to COM port 9, the ASI stage has maintained a stable connection on COM port 13 without interruptions and uncontrolled stage movements are no longer occurring.

docs/source/04_faq/troubleshooting/troubleshooting_home.rst

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+===============
+Troubleshooting
+===============
+
+
+.. _troubleshooting-home:
+
+In this section, we outline some common challenges encountered in setting up a microscope system and provide solutions to address these issues effectively.
+
+.. toctree::
+   :maxdepth: 1
+
+   01_proxy
+   02_usb_connectivity
+
+