sgtlib 3.4.0b0

A software tool for graph theory analysis of microscopy images.

StructuralGT

A software tool that allows graph theory analysis of nanostructures. This is a modified version of StructuralGT initially proposed by Drew A. Vecchio, DOI: 10.1021/acsnano.1c04711.

Installation

1. Install as software

• Download link: https://forms.gle/UtFfkGGqRoUjzeL47
• Install and enjoy.
• 5 minute YouTube tutorial: https://www.youtube.com/watch?v=bEXaIKnse3g
• We would love to hear from you, please give us feedback.

2. Install via source code

Therefore, please follow the manual installation instructions provided below:

• Install Python version 3.13 on your computer.
• Git Clone the branch DicksonOwuor-GUI from this repo: https://github.com/compass-stc/StructuralGT.git
• Extract the source code folder named 'structural-gt' and save it to your preferred location on your PC.
• Open a terminal application such as CMD.
• Navigate to the location where you saved the 'structural-gt' folder using the terminal.
• Execute the following commands:

cd structural-gt
pip install --upgrade pip
pip install -r requirements.txt
pip install .

2(a) Executing GUI App

To run the GUI version, please follow these steps:

• Open a terminal application such as CMD.
• Execute the following command:

StructuralGT

2(b) Executing Terminal App

Before executing StructuralGT-cli, you need to specify these parameters:

• image file path or image directory/folder: [required and mutually exclusive] you can set the file path using -f path-to-image or set the directory path using -d path-to-folder. If the directory path is set, StructuralGT will compute the GT metrics of all the images simultaneously,
• configuration file path: [required] you can set the path to config the file using -c path-to-config. To make it easy, find the file sgt_configs.ini (in the ''root folder'') and modify it to capture your GT parameters,
• type of GT task: [required] you can either 'extract graph' using -t 1 or compute GT metrics using -t 2,
• output directory: [optional] you can set the folder where the GT results will be stored using -o path-to-folder,
• allow auto-scaling : [optional] allows StructuralGT to automatically scale images to an optimal size for computation. You can disable this using -s 0.

Please follow these steps to execute:

• Open a terminal application such as CMD.
• Execute the following command:

StructuralGT-cli -d datasets/ -c datasets/sgt_configs.ini -o results/ -t 2

OR

StructuralGT-cli -f datasets/InVitroBioFilm.png -c datasets/sgt_configs.ini -t 2

OR

StructuralGT-cli -f datasets/InVitroBioFilm.png -c datasets/sgt_configs.ini -t 1

References

• Drew A. Vecchio, Samuel H. Mahler, Mark D. Hammig, and Nicholas A. Kotov ACS Nano 2021 15 (8), 12847-12859. DOI: 10.1021/acsnano.1c04711.