Place your images into HECD1, ACTIN, DAPI subfolders in the folder input_images. Corresponding images should have the same name.

Modify parameters.R and double click on 'Run_segmentation.bat' to run the segmentation. Resulting segmentation should then appear in output_dir. Then double click on 'Run_analyse.bat' to obtain a file output_dir/data.txt which you can open in Excel.

Error: Access denied

Solution: If you have a firewall, it might be blocking the execution of the programs. Try disabling it. If the firewall is indeed the issue, a proper install for R and its dependencies would be a safer long-term solution.

Keraudren, K., Spitaler, M., Braga, V. M., Rueckert, D., & Pizarro, L.: Segmenting Epithelial Cells in High-Throughput RNAi Screens, MIAAB 2011.
PDF code slides