Hello, I am following this tutorial for my 3d image analysis https://github.com/CellProfiler/tutorials/tree/master/3d_monolayer . I am very new at this and have followed it exactly. I am trying to count number of nuclei within GFP+ cytoplasm and get the volume of that GFP+ area. I will attach an image example below. My first issue is I keep on getting an error message that reads "error while processing erosion: footprint array has incorrect shape and gives me the option to continue processing. What does this mean and how can I fix it?
Also is there a way to get an excel type of file or data table that includes the number of nuclei and the volume of the GFP+?
Thank you for the help, I really appreciate it. This has been quite a difficult process for me to learn any tips would be great.3d_2wkrpapsesg_xy1_ch2.tif (10.2 MB)
3d_2wkrpapsesg_xy1_ch1.tif (10.2 MB)