Re: average above threshold
Posted by
Glen MacDonald-2 on
URL: http://imagej.273.s1.nabble.com/average-above-threshold-tp3689549p3689551.html
I think the alternatives are to plot the integrated intensity profile of the thresholded stack, or to create a single frame 3D Mean projection limited to a threshold.
Regards,
Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923 USA
(206) 616-4156
[hidden email]
On Jan 27, 2010, at 9:26 AM, Pablo Manuel Jais wrote:
> Glen MacDonald wrote:
>> Hello,
>> Is it possible in ImageJ to create an Average projection over the z-axis
>> that only includes pixel intensities above threshold? We would like to
>> get an average intensity plot along a structure but the tissue section is
>> not completely flat.
>>
>> thanks,
>> Glen
>
> I'm far from being an expert here, but I don't think there's an easy way
> to do that. If I understand correctly, you want the Z projection to
> average each column of pixels, but only taking into account those values
> that are above the threshold. That is, if a column has the values
> 10,20,30,40,50 and your threshold is 35, you want to get (40+50)/2, right?
>
> I just tried thresholding an image and using Process->Math->NaN
> Background. This takes all pixels below the threshold to NaN. My idea was
> that maybe the Z projection ignored the NaN values when calculating the
> average. However, it doesn't, the average results to NaN too (I think this
> is on purpose, though).
>
> You might need to hack the Z projection function to make a new kind of
> average. Check the source if you feel confident, or ask for help. Maybe
> someone can give you further advice.
>
> Hope this helps,
> Pablo