glowtracker 0.9.0

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

GlowTracker

GlowTracker is a macroscope 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

Install the correct environment

1. Install Conda [Link]

2. Create environment

   • Using Mamba (faster, recommended)
     1. Install Mamba from [Link]
     2. Create environment:

        mamba env update -n macroscope --file StageEnvironment.yml
        

   • Using Conda

     conda env create --file StageEnvironment.yml
     

3. Activate the environment:

   conda activate macroscope
   

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

   • pylon Camera Software Suite
   • pylon runtime library

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

6. After finished installation, the software can be started by

   python glowtracker/__main__.py
   

Device Setup

Stage

In macroscope.ini, specify the connection port name to your Stage. In Windows, this is usually port = COM3. In Linux, usually port = /dev/ttyUSB0

Camera

In macroscope.ini, specify the path to your pylon default camera setting default_settings. 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 macroscope 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'.