This repository contains data and codes for image and statistical analysis of the paper:
"Screening clinical Candida albicans isolates for invasiveness by mimicking the human environment"
By

Clément Vulin, Julian Sutter, Tiziano A. Schweizer, Federica Andreoni, Julian Baer, Willy Isao Steiger, Alexandra Bernasconi, Karl Bulut, Roger D. Kouyos, Brunella Posteraro, Maurizio Saunguinetti, Annelies S. Zinkernagel

preprint: https://doi.org/10.1101/2024.05.27.596042

List of files and content:
01_OriginalTraining => files for original training of the Elastic model
01_OriginalTraining.zip => zip of the above
AllColoniesDat.mat => 15325x35 extracted data table for the filamentation experiment
AreaMembranes.xlsx => membrane data for figure 4
DataUsedForPCA_downstream.mat => short version of AllColonies.dat, used for the PCA analysis
FirstSegIlastik.ilp => Ilastik segmentation pipeline (first step)
MatlabAnalysis => functions for Matlab analysis (images extraction + PCA)
SecondSegIlastik.ilp => Ilastik segmentation pipeline (first step)
Single colony segmentation pipeline => description of the segmentation pipeline