Alternatively to the suggestion from @CellKai,
automatically reading in the cell bodies might work with the following macro (at least on the provided image).
To use the macro do the following:
- get Fiji as descibed by @CellKai
- press [Shift] + N (now the script editor window should open)
- paste the macro below in that window (make sure in the “Language” menu "IJ1Macro is selected.
originalImage = getTitle();
duplicate = getTitle();
run("Gaussian Blur...", "sigma=1 stack");
run("Z Project...", "projection=[Max Intensity]");
projection = getTitle();
run("Subtract Background...", "rolling=15");
run("Auto Threshold", "method=IsoData white");
run("Analyze Particles...", "size=10-Infinity pixel show=Nothing clear add");
run("Plot Z-axis Profile");
- open your image stack
- press the run button in the script editor
- in the resulting plot window activate the [Live] button (turns red)
- select your image (to activate it)
- select the individual ROIs (the numbers in the ROI Manager and you should see the profile changing.
In addition, if you need the values you can then in the next step go to:
→Analyze →Set Measurements and activate the checkboxes related to intensity (Mean would be enough) as shown below.
Then go in the ROI Manager to >>More and Multi Measure
specify the popup dialog as shown
and press Ok and you get all values for all slices and ROIs