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Re: average above threshold

Posted by Glen MacDonald-2 on Jan 29, 2010; 6:28pm
URL: http://imagej.273.s1.nabble.com/average-above-threshold-tp3689549p3689555.html

That is a good point although the results may represent absolute amount of label, the influence of unstained structures such as blood vessel lumina or unstained cell types on label distribution would be lost, since they are "0".  In this particular instance, the sections aren't entirely flat, but the confocal images are through their entirety.

It will be interesting to compare results for this particular application.

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
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On Jan 29, 2010, at 3:50 AM, Gabriel Landini wrote:

> On Friday 29 Jan 2010  11:43:46 you wrote:
>> This worked:
>> Duplicate stack
>> threshold, dark bg
>> make binary
>> divide by 255
>> multiply result with original to set pixels <t to 0
>> Z-axis projection to sum slices - automatically creates 32-bit result.
>
>> The structure of interest in each stack is at an angle, and Plot Profile
>> doesn't work with rectangular ROIs created with the Polygon tool.  Which
>> means the final step is to draw a line along the structure's axis to set
>> image rotation so we can use a rectangular ROI to get an averaged profile
>> plot of the summed intensities.
>
> However the "sum intensities" should be divided by the "sum of binary slices
> with values 0 and 1" because the first sum is not guaranteed to be due to the
> same number of contributing slices. (not sure I am being clear).
>
> Let's say for a pixel, your sum of 200 can be contributed by 4 slices with a
> value of 50 in each slice, or by 2 slices with 100 in each slice.
> In the first case your average should be 50 in the second 100.
>
> Cheers
>
> Gabriel