ImageJ : analyse a folder of images and get results on exel sheet

Hi !

I am new to this website, french and new to ImageJ.
I made a macro to analyse images and calculate an area percentage.

run(“Duplicate…”, “title=C1”);
run(“Split Channels”);
selectWindow(“C1 (blue)”);
imageCalculator(“Subtract create”, “C”,“C1 (red)”);
selectWindow(“Result of C”);
run(“Make Binary”);
run(“Set Measurements…”, “area redirect=None decimal=2”);
run(“Analyze Particles…”, “size=0-Infinity circularity=0.00-1.00 show=Nothing clear summarize”);

I have a lot of images and it does not work when I want to use Process>Batch>Macro…

What I would like is a way to analyse all the images I have in a folder and then get all the results in the same exel sheet.

Thanks for your help,



Hi Apolline,

you could try to remove “clear” from the line :

because it clears the results table when analyzing a new image (just make sure it’s cleared when you start the batch)

I hope it will help you.




Thanks for your answer, I tried it but it didn’t work.

I have the message:

image not found in line 5
image Calculator “Substract create”, ,“C1(red)”

Peut-etre vous pouvez essayer CellProfiler pour cette projet? Ok, that is probably the extent of my french from high school :slight_smile:

Try a pipeline of these modules:

  1. The first 4 default modules help you specify what images you want to process and which channels are which. Drag and drop your folder into the Images module to get started. Then set NamesAndTypes.
  2. ColorToGray can split channels.
  3. I’m not sure what you are trying to do from there, but if it’s identifying individual objects, the try IdentifyPrimaryObjects. If measuring intensities within each object, then MeasureObjectIntensity. If you need to subtract images, then ImageMath.
    N. ExportToSpreadsheet!

Your french still great!
Thanks for your answer.
I tried to download Cellprofiler but it didn’t work I think my version of Windows is too old.
So I will keep trying to improve my macro on imageJ.

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