Contents Data: This folder contains all the raw 3D images in Zeiss native fomat ".czi", 2D masks of the chip and the machine learning-based models to extract the mask. It includes two zip files: Data-Epithelial.zip and Data-Vascular.zip, each containing the recorded images from either the epithelial compartment or the vascular compartment of the chip, respectively. Each file contains two folders named Image and Mask. - The Image folder contains all the raw images. For the epithelial compartment, it includes the minimum intensity projection of the brightfield channel of epithelial images, from which the epithelial mask was obtained. For the vascular compartment, it contains the realigned images of the vascular side and the maximum intensity projection of the DAPI channel, from which the endothelial mask was derived. - The Mask folder contains the corresponding 2D masks of the chip area, excluding artifact regions and edge areas. Additionally, it includes the trained WEKA model used for mask extraction (both classifier and associated data files). Codes: this folder contains the image analysis scripts and workflows. it includes 4 files; -Analysis workflow.jip: 3 compartments are defined which estimate ZO-1 damage area fraction, epithelial tissue thickness and vascular cell density. -Tiles realignment-Vascular.ijm: ImageJ macro for vascular tiles realignment. -Chip mask by weka-Epithelial.ijm: script for training a weka model for prediction of mask area for epithelial data. -Chip mask by weka-Vascular.ijm: script for training a weka model for prediction of mask area for endothelial data. How to run the codes: To install ImageJ, please visit https://imagej.net/ij/download.html To open a macro, use the File>Open or Plugins>Macros>Edit commands, or drag and drop it on the "ImageJ" window. Please make sure the following packages are installed: - 3D ImageJ Suite - Biomedgroup - IJPB-plugins - BoneJ - ImageScience - ResultsToExcel for more information on how to install plugins, please visit https://imagej.net/plugins/ Detailed information are provided as comments in the scripts! please visit https://jipipe.hki-jena.de/ on how to run a JIPipe workflow.