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Repository for code developed for my REIT4841 Thesis Project

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VolumeSegmentation

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]

Python Environment

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.

  1. Create the Environment

py -3.11 -m venv .env

  1. Activate the Environment

./.env/scripts/activate

  1. Install the required dependencies

python -m pip install -r requirements.txt

  1. 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

Demo GUI

In order to run the unified demo GUI, complete the following steps:

  1. Ensure a Python 3.11 environment with the required libraries is created and activated following the steps above.
  2. Ensure you are in the ./DEMO directory

cd demo

  1. Run the GUI script:

python ./demo_gui.py

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Repository for code developed for my REIT4841 Thesis Project

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