Functions used for the computational experiments appearing in the papers "Persistent entropy: a scale-invariant topological statistic for analyzing cell arrangements" and "Characterising epithelial tissues using persistent entropy".

The functions are the following: - reduce_cells.m: contains the spiral algorithm for normalizing the number of cells in the image. (matlab) - persistentEntropy: take a barcode and calculate its persistent entropy. (R)

The scripts with the code of the experiments are: - obtain_point_cloud.m: read the data, run reduce_cells.m and write the result. - generateFrame.R: calculate the data.frame containing the entropy values of all images and a normalization number n = 5, 10, 15... up to 385. - generateBarcode.R: calculate all barcodes of a type of cell. - generateFigures: create a boxplot with the persistent entropy value

The workspace.Rdata file can be loaded to obtain the persistent entropy values for all tissue images and different normalization numbers. You can find the sum of the length of all bars in each barcode as well. Please, feel free to use this values as long as you cite our paper.

Unfortunately, I am not the owner of the data, so I cannot provide you the images nor the point clouds (these folders are empty). However, you can use the barcodes appearing in the namesake folder.

If you would like to talk with the data owner and ask for permission to use it, please, contact us via email: msoriano4 (at) us (dot) es