http://imagej.273.s1.nabble.com/setting-auto-threshold-in-a-macro-tp3687423p3687426.html
> Rasband, Wayne (NIH/NIMH) [E] a écrit :
>> 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
> back the lines I had commented that convert the image to 8-bit before
> 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
> of 6 images are properly thresholded by the macro.
>
>
http://www.woofiles.com/dl-201950-Zdk2DrwO-MAX1038w3DAPI.tifThe ImageJ 1.44e8 daily build fixes a bug that caused setAutoThreshold("Default dark") to sometimes not generate the expected threshold for an image with a sharp peak in its histogram.