That ought to fix my problem with the autothreshold - thanks, Justin.
Anybody have any advice regarding the volume measurement?
Aaron
On Thu, 6 Dec 2007 14:12:20 -0600, Justin McGrath <
[hidden email]>
wrote:
>Does the autothreshold not work because it doesn't include 255? If
>that's the problem, you can use
>setAutoThreshold();
>getThreshold(lower,upper);
>setThreshold(lower,255);
>
>Which would get the bottom cutoff automatically then set the upper to
>255. If the bottom cutoff isn't good, then you might try some of the
>threshold plugins listed on the ImageJ website, or you can come up
>with your own criterion and make a macro or plugin for it. I wrote a
>macro once that cut off the leftmost peak of the histogram, which in
>my images was always unwanted. I could find it if sounds useful to
>you. However, it's kind of shoddy coding.
>
>Justin
>
>On Dec 6, 2007 9:47 AM, Aaron Johnson <
[hidden email]> wrote:
>> Hello, I'm interested in finding a way to do a volume measurement of an
8-
>> bit grayscale stack (usually between 15-20 images) coming from a
confocal
>> microscope. The structure I'm measuring (ACh receptor) is fairly
>> contiguous and could be characterized as blob-shaped. My main questions
>> are:
>>
>> 1) What are your recommendations regarding thresholding? I always want
to
>> capture the max (255), and am more concerned about finding an automated
>> way of finding the minimum. The "auto-threshold" doesn't work for me.
>>
>> 2) What do you recommend for the volume measurement? I've tried voxel
>> counter with some success, but I'm wondering if there are other easy
ways
>> to do this, if for no other reason than to confirm my measurements with
>> voxel counter.
>>
>> Thanks!
>> Aaron
>>
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