Setting a default threshold, batch processing

[ekading]

Hello,  I am new to ImageJ/programming and am experimenting with recording
my own macros and then applying them to batch processing.

I need to analyze particles for area, greyscale mode/mean, major axis,
minor axis.  There are about 70 images per batch with about 10 particles
per image, so I would ideally like to create a macro that can be used to
quickly batch process.

My problem is, I would like to set the threshold for the second slider
under Brightness to a set value and analyze all images with those specific
settings.

I can export the Threshold macro data to the recorder and apply this to one
image, however it fails when I try batch processing.

I would prefer not to work with 8 bit images as I have been trying that and
losing data.

Does anyone have any ideas how to set a custom, default threshold and apply
it to batch processing?

Thank you!
Emily

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[Citron, Bruce]

You can use the setThreshold command, e.g., setThreshold(600, 4096);

Sometimes it works better if the threshold is automatically set using one
of the built in algorithms, e.g.,
setAutoThreshold(³Default dark²);
or
setAutoThreshold(³Intermodes dark²):

You can try a few options and see which gives you the best signal to noise.

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