This repository documents my work for my honours thesis project (REIT4841) at the University of Queensland. The scripts within are written for the paper "Algorithmic Volume Segmentation of Two-photon Microscopy Z-stacks".
- Ryan Gibbons
NOTE: Without necessary data files, the scripts in this repository will NOT run as expected. Cloning this repository is not sufficient to run segmentations, as segmentations require a 2D segmented z-stack .csv file.
Contact for questions: [email protected]
Each sub-folder has requirements to run its own environment, however at the root level a requirements.txt
file has been provided that will allow all scripts to be run in a single environment.
- Create the Environment
py -3.11 -m venv .env
- Activate the Environment
./.env/scripts/activate
- Install the required dependencies
python -m pip install -r requirements.txt
- Ensure your interpreter is set to use this environment (for quick run in VSCode)
In VSCode,
ctrl+shift+p
will allow you to select an interpreter. The interpreter path should be manually defined as:./.env/scripts/python.exe
In order to run the unified demo GUI, complete the following steps:
- Ensure a Python 3.11 environment with the required libraries is created and activated following the steps above.
- Ensure you are in the ./DEMO directory
cd demo
- Run the GUI script:
python ./demo_gui.py