Wide-ranging changes #2
Description
Here a complete descrition of what the code is expected (in my opinion) to do.
I (the user) upload data coming from the Fiji's CellCounter extension into the working directory. Those files are .xml and are preceeed by the "CellCounter" prefix. The code should look only for them to make downstream calulations. The next step the code should do is to look into these .xml files and extract occurences of the different cell markers (i.e. ki67+, sox10+, ...). Those occurences should be stored into a table (I don't tihnk a matrix is such flexible in this case) that will have cell markers as column names and the anatomical region (amygdala, neocortex, ...) as row names. At the end of the process I expect to have a table containing the occurrences of all cell markers in all anatomical regions coming from those CellCounter .xml files. Additionaly, it would be useful to add a couple of columns referring to the area (mm^2, should be always the same for all photos so it is ok if it is specified only once) in which the photo was taken and, most importantly, the density of cells (since there is the area and the number of cells is not so difficult).
The latest step is to have this table outputted as an .xlxs file so it is possible to download and open it with excel.
Tell me if everything is clear.