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macrosimagej

set threshold as a function of autoThreshold

I have written a macro for ImageJ/FIJI to deconvolve my confocal microscopy images and run the "3D Object Counter" plugin. The macro successfully runs all required commands and saves all required data in the specified places.

However, I have found that the 3D-OC autothreshold (as shown in the plugin dialog box) is to stringent resulting in objects being lost or divided. To remedy this I would like to reduce the autothreshold by a predetermined function something similar to what was done here (from:How to get threshold value used by auto threshold Plugin) which resulted in this code: 

setAutoThreshold();
   getThreshold(lower,upper);
   v=setThreshold(lower,upper*0.5);
   run("3D Objects Counter", "threshold="v" slice=10 min.=400 max.=20971520 objects statistics summary");

The idea was to call the AutoThreshold values, modify them and set them to a variable. However when these lines are run the following error is returned:

Number or numeric function expected in line 3.
v=<setThreshold>(lower,upper*0.5);

And if the variable is inserted directly into the threshold key for run(3D-OC) the following msg is encountered:

Numeric value expected in run() function
Key:"threshold"
Value or variable name:"setThreshold(lower,upper*0.5"

Any suggestions or help on how to designate the 3D-OC threshold value as a variable as described would be greatly appreciated (as would any work arounds of course :) ).

Cheers

Edit: After testing Jan's response below (which works perfectly), it appears I need to call the threshold set by the 3D-OC plugin. Anyone know how to do this?

Solution

  • The getThreshold(lower, upper) function returns the lower and upper threshold levels in the provided variables. There is no need to assign any value to a new variable, and as you observed, setThreshold does not have any return value.

    Instead, you can use the value(s) returned from getThreshold and use them as parameters in the run method (in the correct way, by string concatenation, see here):

    setAutoThreshold();
getThreshold(lower, v);
run("3D Objects Counter", "threshold=" + v + " slice=10 min.=400 max.=20971520 objects statistics summary");

    Alternatively, you can use &v in the second parameter to avoid string concatenation in the last line (see the documentation for the run() macro function):

    run("3D Objects Counter", "threshold=&v slice=10 min.=400 max.=20971520 objects statistics summary");

    You might have to use the lower instead of the upper threshold value, depending on whether you count bright or dark objects.