A spectrum of p-atic symmetries and defects in confluent epithelia

This is a python code that calculates p-atic defects for p 2,3,4,5 or 6 for experimental data given as greyscale images (every cell has one value, the background has the value 0). This code belongs to the following publication: Lea Happel, Griseldis Oberschelp, Anneli Richter, Gwenda Roselene Rode,Valeriia Grudtsyna, Amin Doostmohammadi, Axel Voigt: A spectrum of p-atic symmetries and defects in confluent epithelia, published in SoftMatter in 2026 (doi: 10.1039/D5SM01010A) The program was written with Python 3.11, it requires the following packages: copy csv cv2 gc lic matplotlib numpy os pandas scipy seaborn shapely skimage vtk The program expects a folder in the base_directory which is called "image_data" and which contains *.tif files for the single frames. This base_directory is then needed as command line argument for detect_contours and Orientation_field_Linear. First, execute detect_contours to calculate the p-atic orientations of the cells. Then, execute Orientation_field_Linear to calculate the defects in this p-atic fields. For a more detailed description of the used algorithms, please refer to the Methods section of the correspond publication. Please note that the plotted images are mirrored on the y-axis with respect to your input greyscale images.