Run gene_heatmap_generator, and mergedgene_heatmap_generator, this will create Tiff files that you can inspect. 

You'll want to create Tiff files for multiple lungs by switching which tsv file you are looking at. Create three folders (Lung1...) and populate them with the files you want. Then use genecounts_medial_epiandmes.jl to try segmenting and creating plots based on epithelial/mesenchymal markers like EPCAM. 

If you want to show multiple tiffs at the same time, one way to do that is to load up to 4 tiffs into imageJ and use the benraystipple_imageJmacro macro.