Re: help with outdated macro

Posted by Gabriel Landini on
URL: http://imagej.273.s1.nabble.com/help-with-outdated-macro-tp5003326p5003328.html

On Monday 10 Jun 2013 19:56:15 Elyse Aurbach wrote:

> Hello,
>
> My lab uses ImageJ to quantify greyscale images. I joined the lab and
> inherited the attached macro to help take background measurements The macro
> was written in 2005, and with ImageJ version 1.34h through versions
> 1.44p-ish, this macro is sufficient to measure what my lab calls the
> "background" of a selection in the image, then threshold the image such
> that the "signal" is defined as the mean of the selection plus 3.5 times
> the standard deviation of the selection. From there, in the earlier
> versions, the macro then calls the Threshold function to set a mask on the
> image, such that only pixels with an intensity value above the "signal"
> threshold are included in subsequent measurements. The issue is that this
> macro does not work the same way in newer versions of ImageJ--the macro
> works fine to set the threshold value, but the mask is never created. Is
> this a matter of the source Threshold function changing? Is there a second
> "mask" function that should be called? Is there something I'm not seeing?

You are probably missing the "Standard deviation" box ticked in
Analyze>Set Measurements.
If it is not ticked, then the value is not extracted and you cannot compute
the background value.

Cheers
Gabriel

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