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QT3 Quantum Light Microscope

The following instructions are for setting up the QLM microscope machine with the QT3 software.

These instructions should also work for other setups that use similar hardware.

We utilize Anaconda for managing our python environments.

Install Anaconda

First, one should install Anaconda if it's not already installed.

Launch Anaconda.

Create New Environment.

If you are simply a user of the code, that environment may be called something like "qt3-production" to indicate that you are using the "production" level qt3 code and do not intend to develop new features or fix bugs.

If you need to develop new code for one of the qt3 software repositories, a better environment name may be "qt3-develop-feature-X", or similar, depending on your project and scope.

In either case, the QLM also needs some external divers. If you are setting up a new machine from scratch, you will need to install these. If you are a user on the QLM machine that is already in use, these drivers are likely already installed.

Production Environment Setup

Once the NIDAQ and SpinCore drivers are installed, do the following:

  1. Open Anaconda
  2. Activate your production environment
  3. Launch a Powershell
  4. Ensure the powershell prompt displays the correct environment name
  5. Use pip to install
  • > pip install qt3-utils

If installation is successful, you should be able to run the GUI applications defined in qt3-utils.

The powershell is recommended at this time because we do not have automatic application deployment. Also, running the GUI applications from the Powershell provides a stdout for the application to set log messages. These log messages are useful as a user to see that the application is running and this is where messages will be displayed when errors occur.

Develop Environment Setup

Once the NIDAQ and SpinCore drivers are installed, do the following:

  1. Open Anaconda
  2. Activate your development environment
  3. Launch a Powershell
  4. Ensure the powershell prompt displays the correct environment name
  5. Navigate to a location on the filesystem where you want to perform development
  • For example, > mkdir \Users\YOURNAME\projects; cd projects
  1. Clone the git repository of interest
  • For example > git clone https://github.com/qt3uw/qt3-utils

Development after this step is up to you. You can install PyCharm or VSCode from Anaconda, or work with something lighter like Atom.

When working on windows, you may need to set the execution policy of the Powershell so that it can run Anaconda configuration scripts when opening the Terminal in PyCharm (and possibly other IDEs). See this page for more information. The command to run is

> Set-ExecutionPolicy -ExecutionPolicy Unrestricted -Scope CurrentUser

Laser Power Control

Control of laser power via ND filter wheel is done using qt3laserpowercontrol. This software controls an ARDIUNO board that is connected via USB to the QLM machine. The software needs to be installed onto the ARDUINO board and then launched separately from the command line.

Production Conda Environment Snapshots

The following links to minimal conda environments on the QLM machine that were known to work. These environments pin down specific versions of software and should be able to recreate environments