This simple script allows the user to obtain both a .png file showing the identified cells and their oval orientations, as well as a graph with the polar histogram of the orientations of all cells in the provided input file.
Simply provide an input picture of some cells or blobs (for example, from a microscope). On a command line, run:
python identify_cells.py -i input_file.tiff -oh histogram.dat -of results.svgOpen the script and change the input variables (lines 14-25) to change the overall aesthetic look of your results.
In order to bypass installing all necessary pre-requesite packages, you can use the Cell Orientation Identificator directly on Google Colab!
For more information or help, please contact [email protected]