This repository focuses on the extraction of growth images of biological organisms on petri dishes and the calculation of dynamic features such as area, perimeter, circularity and fractal dimension.
Folder s-petana: Compatibility with experimental data from scanner-derived raw images.
- Collection of scipts related to bio-growth in petridishes
Folder i-petana: Compatibility with experimental data such as videos.
- Script for conversion of video to images.
- Image extraction
- Calculation of area, perimeter of growth contour
- Calculation of circularity based on area and perimeter of growth contour
- Calculation of Fractal dimension of growth contour
- Description of core function features related to Image_Extraction_Routine & Dynamical_Parameter_Extraction_Routine
- Description of Main_Execution_Blocks for Image_Extraction_Routine & Dynamical_Parameter_Extraction_Routine
- PyPETANAv1.0.0 main documentation: Sengupta, S. (2024). PyPETANAv1.0.0 Documentation (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.13165895
This research was undertaken in part thanks to funding from the Alfred P. Sloan Foundation (Matter-to-Life program). I thank Nirosha J. Murugan and Philip Kurian for helpful discussions with regards to Fricker Software and fractal dimensions, respectively.
- New features, bug fixes, documentation, tutorial examples, code testing is welcome in the developer community!