A spectrum of p-atic symmetries and defects in confluent epithelia
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| Natura: | Recurso digital |
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2026
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| _version_ | 1866901675968561152 |
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| author | Happel, Lea Oberschelp, Griseldis Richter, Anneli Rode, Gwenda R. Tobin, Brendan |
| author_facet | Happel, Lea Oberschelp, Griseldis Richter, Anneli Rode, Gwenda R. Tobin, Brendan |
| contents | <p>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).</p> <p> </p> <p>This code belongs to the following publication:</p> <p>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)</p> <p> </p> <p>The program was written with Python 3.11, it requires the following packages:</p> <p>copy</p> <p>csv</p> <p>cv2</p> <p>gc</p> <p>lic</p> <p>matplotlib</p> <p>numpy</p> <p>os</p> <p>pandas</p> <p>scipy</p> <p>seaborn</p> <p>shapely</p> <p>skimage</p> <p>vtk</p> <p> </p> <p>The program expects a folder in the base_directory which is called "image_data" and which contains *.tif files for the single frames.</p> <p>This base_directory is then needed as command line argument for detect_contours and Orientation_field_Linear.</p> <p> </p> <p>First, execute detect_contours to calculate the p-atic orientations of the cells.</p> <p> </p> <p>Then, execute Orientation_field_Linear to calculate the defects in this p-atic fields.</p> <p> </p> <p>For a more detailed description of the used algorithms, please refer to the Methods section of the correspond publication.</p> <p>Please note that the plotted images are mirrored on the y-axis with respect to your input greyscale images.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18175147 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | A spectrum of p-atic symmetries and defects in confluent epithelia Happel, Lea Oberschelp, Griseldis Richter, Anneli Rode, Gwenda R. Tobin, Brendan <p>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).</p> <p> </p> <p>This code belongs to the following publication:</p> <p>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)</p> <p> </p> <p>The program was written with Python 3.11, it requires the following packages:</p> <p>copy</p> <p>csv</p> <p>cv2</p> <p>gc</p> <p>lic</p> <p>matplotlib</p> <p>numpy</p> <p>os</p> <p>pandas</p> <p>scipy</p> <p>seaborn</p> <p>shapely</p> <p>skimage</p> <p>vtk</p> <p> </p> <p>The program expects a folder in the base_directory which is called "image_data" and which contains *.tif files for the single frames.</p> <p>This base_directory is then needed as command line argument for detect_contours and Orientation_field_Linear.</p> <p> </p> <p>First, execute detect_contours to calculate the p-atic orientations of the cells.</p> <p> </p> <p>Then, execute Orientation_field_Linear to calculate the defects in this p-atic fields.</p> <p> </p> <p>For a more detailed description of the used algorithms, please refer to the Methods section of the correspond publication.</p> <p>Please note that the plotted images are mirrored on the y-axis with respect to your input greyscale images.</p> |
| title | A spectrum of p-atic symmetries and defects in confluent epithelia |
| url | https://doi.org/10.5281/zenodo.18175147 |