Contents

Data: this folder contains all the 3D images after deconvolution and correction for chromatic aberration (using the software Huygens Professional)
      it includes 2 folders; Wild type and Clinical isolate inside each you find the following folders;
	 -BF (Brightfield images)
	 -Microcolony
	 -Nuclei

Codes: this folder contains the image analysis scripts
       it includes 3 folders;

	  -3D Segmentation of Microcolony
		"Microcolony_Segmentation.ijm" reads the preprocessed microcolony data, saves the sagmenation after branch reconstrcution
		"Microcolony_Morphometrics.ijm" saves an .xslx file containing the 3D morphological characterization

	  -Epithelial Tissue Architecture
		"Chip_Membrane_Position.ijm" reads the BF data, estimate the membrane position and saves the results
		"Nuclei_Segmentation.ijm" reads the preprocessed nuclei data and save the 3D segmentation
		"Epithelial_Tissue_Position.ijm" reads the 3D nuclei segmentation and estimates epithelial tissue position and save the result
		"Epithelial_Tissue_Position_Interpolation.ijm" reads the epithelial tissue position and interpolates areas in between nuclei and save the result
		"Epithelial_Tissue_Thickness.ijm" saves the epithelial tissue thickness

	  -3D Localization of Microcolonies
		"3D_Stack_Classification.ijm" reads the quantifications of the previous step and classifies the stack
		"3D_Microcolony_Localization.ijm" saves the results of multi-colocalization between microcolony and tissue

	  -Tissue integrity
		"Fluorescence intensity measurement.ijm" measures the MFI of DAPI
		"Area fraction analysis of E-cadherin and CD31.ijm" quantifies the area fraction of E-cadherin and CD31

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
- Masks from Rois
for more information on how to install plugins, please visit https://imagej.net/plugins/
Detailed information are provided as comments in the scripts!