http://imagej.273.s1.nabble.com/setting-auto-threshold-in-a-macro-tp3687423p3687425.html
> On Jul 29, 2010, at 1:44 PM, Crowell Elizabeth wrote:
>
>
>> Hello group members,
>>
>> I have yet another question for you.
>> I am trying to write a macro (attached) that will select particles of a
>> defined size in my images (in this case, nuclei). I make a projection
>> of my stack, try to auto threshold it with a dark background, make it
>> binary, and run analyze particles.
>>
>> When I adjust the threshold manually, clicking the auto button with the
>> "dark background" box checked gives me exactly the result desired.
>> Therefore I think my images are of sufficient quality to let me
>> threshold them automatically.
>>
>> However, the auto threshold function is not functioning properly in the
>> macro. The thresholding is not restrictive enough (it takes a wide
>> spectrum of gray values around the particles that just represent
>> noise). When I put in a wait function and run the macro while batchmode
>> = false, I can see that in the threshold window, the "dark background"
>> box is never checked. If I run the macro with the waitForUser line, the
>> image is thresholded correctly initially, and then changes to an
>> incorrect, non-restrictive threshold when the dialog box appears. So
>> there is something really fishy going on!
>>
>> How can I instruct ImageJ to adjust the threshold automatically with a
>> dark background? Apparently, the line "setAutoThreshold("Default
>> dark");" is not sufficient.
>>
>> Thank you in advance for your help,
>>
>
> What version of ImageJ are you using? There are two recent setAutoThreshold() bug fixes listed in the release notes (
http://rsbweb.nih.gov/ij/notes.html).
>
> v1.44c:
> Fixed a bug in the setAutoThreshold() macro function that caused the threshold level to be one less than the level set by the "Threshold" widget when "Dark background" was enabled.
>
> v1.43u:
> Fixed a bug that caused the setAutoThreshold() macro function to not work correctly with 16 and 32 bit images that were not using the default display range.
>
> -wayne
>
Now I am using version 1.44d, but I still have the bugs. I also added
thresholding. There is still the exact same behavior. If it helps, I
have posted an example problematic image at the site below. Only 2 out
----------------------------------------------------------------------