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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? Many thanks for any and all help with this issue! All the best, Elyse Aurbach -- Elyse L. Aurbach Ph.D. Candidate, Akil Lab Molecular and Behavioral Neuroscience Institute Neuroscience Graduate Program University of Michigan, Ann Arbor, MI -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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? ... [show rest of quote] 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gabriel,
Thanks so much for your reply! My 'Standard deviation' box is indeed checked--and when I visually look at the Threshold box, the appropriate bounds have been placed on the intensity histogram after using the macro. But the mask doesn't appear over the thresholded image--and if I take a measurement without manually adjusting the mask, it returns null values. I really appreciate your help--do you have any other ideas I can try? Many thanks! Elyse On Mon, Jun 10, 2013 at 4:57 PM, Gabriel Landini <[hidden email]>wrote: > 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 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > ... [show rest of quote] -- Elyse L. Aurbach Ph.D. Candidate, Akil Lab Molecular and Behavioral Neuroscience Institute Neuroscience Graduate Program University of Michigan, Ann Arbor, MI -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On Monday 10 Jun 2013 22:01:20 Elyse Aurbach wrote:
> My 'Standard deviation' box is indeed > checked--and when I visually look at the Threshold box, the appropriate > bounds have been placed on the intensity histogram after using the macro. > But the mask doesn't appear over the thresholded image--and if I take a > measurement without manually adjusting the mask, it returns null values. I > really appreciate your help--do you have any other ideas I can try? After checking Standard Deviation, the macro works here (shows a thresholded range in red) with the Dot Blot image (IJ v 1.47u1 linux 64 bit). Have you tried updating to the daily build? Tried on a different computer? Sorry I have no further suggestions. Regards Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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