UMIC_Toolkit

Common custom Python scripts used for UMIC-related workflows. These workflows have been translated to a GUI for accessibility. Note this is still work-in-progress.

Modules

EMD Converter

Extracts elemental maps as .tiff files from .emd files, provides instructions for stitching using TrakEM2 and enables converson to .ome.tiff-files.

Usage

The GUI can be launched from the command line or packaged into an .exe. First the appropriate environment will have to be created and the repository has to be cloned.

Create environment

Create a conda environment.

conda create --name environment_name

Activate the conda environment.

conda activate environment_name

Clone the repository

Create a directory where you want a clone of the repository and navigate to it. For example:

cd "D:/Github/UMIC_Toolkit"

Clone the repository.

git clone https://github.com/BHPD/UMIC_Toolkit.git
cd UMIC_Toolkit

Install packages

Install the required packages using the requirements.txt file.

conda install --file requirements.txt

Note this requirements.txt is not available yet

Launch GUI

Activate the appropriate environment. Navigate to the directory where the repository is cloned.

python main.py

(Optional) package the GUI into a .exe for convenience

Change the build.spec file such that the relevant absolute paths are correct for your computer. Using PyInstaller:

pyinstaller build.spec --clean