glowtracker 0.11.0

GlowTracker provides a graphical user interface to operate a microscope. The microscope is a hardware setup designed for tracking a small animal in bright field, single or dual epi-fluorescence imaging.

GlowTracker

GlowTracker is a microscope tracking application that has the capability of tracking a small animal in bright-field, single or dual epi-fluorescence imaging. The application interface provides controls over linear Zaber stage movement and Basler camera properties. Please visit the documentation website on how to build the setup from scratch and how to operate the software at https://scholz-lab.github.io/GlowTracker/.

Getting started

Software Setup

1. Create and activate a python environment using venv or Conda.

   • Using venv

     GlowTracker requires python version of at least 3.10. If you do not have one, please download from [Python].

     1. Create the environment

        python -m venv glowtracker
        

     2. Activate the environment

        source glowtracker/Scripts/activate
        

   • Using Conda

     1. Install Conda [Link]
     2. Use conda to create a new python environment named glowtracker.

        conda create -n glowtracker "python>=3.10,<3.12"
        

     3. Activate the glowtracker environment

        conda activate glowtracker
        

2. Install the glowtracker package.

   • Using pip to install from PyPI repository:

     python -m pip install glowtracker
     

   • Or clone and run the package locally.
     1. Clone the pository

        git clone https://github.com/scholz-lab/GlowTracker.git
        

     2. Update the conda environment to download the dependencies

        cd Glowtracker;
        conda env update --file glowtracker/StageEnvironment.yml --prune
        

3. Install the BASLER pylon software and runtime library [Link]

   • pylon Camera Software Suite
   • pylon runtime library

4. (Optional) Install Zaber Launcher for inspecting and updating stage firmware [Link]

5. After finished installation, the software can be started in several ways

   • If you have installed it via pip

     python -m glowtracker
     

     or simply

     glowtracker
     

   • If you have installed it by cloning the package and running them locally

     python glowtracker/__main__.py
     

Device Setup

Stage

In Settings > Stage > Stage serial port, specify the connection port name to your Stage. In Windows, this is usually port = COM3. And /dev/ttyUSB0 for Linux.

Camera

In Settings > Camera > Default camera settings, specify the path to your pylon default camera setting. This is a .pfs file that can be obtained from the pylon Viewer software that you have downloaded.

GUI overview

Code overview

The application is based on the Kivy framework which connects to the microscope hardware. The GUI functionality is implemented mostly in the Kivy file, whereas device functionality is relayed to specific modules.

Known issues

• On Linux systems, accessing serial ports needs to be allowed for the user running the GUI. In Ubuntu and similar systems, the user has to be added to the group 'dialout'.

Supported Operating Systems

• Windows 10, Windows 11
• Ubuntu 16.04 or newer
• macOS Sonoma or newer