Continuing the discussion from Using Read and Write Excel with 3D Manager Results:
I’m still having issues with automating my analysis with MorphoLibJ.
I have segmented an ROI (WholeSpheroid) and wish to quantify the intensity of a protein of interest (ImageName) within that region, before saving those results with the Read and Write Excel plugin.
However, when I run my code I still get an error telling me that the image I wish to quantify is “not a valid choice for input” when running the Intensity Measurements 2D/3D analysis.
I have tried removing the file extension among other things but the window names match perfectly, so I’m a little stuck.
I think I have linked my previous post above, but just to be safe, here is the code that throws an error:
print(ImageName); print(WholeSpheroid); selectWindow("C2-" + ImageName); run("Intensity Measurements 2D/3D", "input=[C2-" + ImageName + "] labels=[" + WholeSpheroid + "] mean stddev max min median mode numberofvoxels volume"); Table.rename("C2-" + ImageName + "-intensity-measurements", "Results"); run("Read and Write Excel", "file_mode=queue_write dataset_label=[Paxillin Quantification]");
I’ve used print statements to check the variables are accurate and they are - as you can see in my previous post (hopefully!). Selecting the window beforehand also doesn’t make a difference. : (
Any ideas on what constitutes a “valid input” for Intensity Measurements 2D/3D? Or what I could change/try to get it accepting my input images?
Any and all suggestions are greatly appreciated!