Measuring only intensities above threshold in stack

[Jacob Keller]

Dear List,

is there a simple way to measure/output only those intensities (or the area
and mean thereof) in each image in a stack which are above a given
threshold? I can do the thresholding, which changes for every image but is
based on the stack histogram, but then I can't output the intensities of
the above-threshold areas, which are changing and moving across the stack.
I feel that there must be a pull-down option for this, but cannot find it...

Any help would be appreciated,

Jacob

--
*******************************************

Jacob Pearson Keller, PhD

Looger Lab/HHMI Janelia Farms Research Campus

19700 Helix Dr, Ashburn, VA 20147

email: [hidden email]

*******************************************

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Christine Labno-2]

Dear Jacob,

Under Analyze --> Set Measurements, check the box that says "Limit to Threshold" and this should do what you want.

Best,
Christine


Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
[phone] (phone)
Please consider the environment before printing this email.

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Jacob Keller [[hidden email]]
Sent: Thursday, March 21, 2013 4:50 PM
To: [hidden email]
Subject: Measuring only intensities above threshold in stack

Dear List,

is there a simple way to measure/output only those intensities (or the area
and mean thereof) in each image in a stack which are above a given
threshold? I can do the thresholding, which changes for every image but is
based on the stack histogram, but then I can't output the intensities of
the above-threshold areas, which are changing and moving across the stack.
I feel that there must be a pull-down option for this, but cannot find it...

Any help would be appreciated,

Jacob

--
*******************************************

Jacob Pearson Keller, PhD

Looger Lab/HHMI Janelia Farms Research Campus

19700 Helix Dr, Ashburn, VA 20147

email: [hidden email]

*******************************************

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Jacob Keller]

Thanks to Wayne Rusband and Christine Labno--got what I wanted!

Jacob Keller

On Fri, Mar 22, 2013 at 12:11 PM, Christine Labno <[hidden email]>wrote:

> Dear Jacob,
>
> Under Analyze --> Set Measurements, check the box that says "Limit to
> Threshold" and this should do what you want.
>
> Best,
> Christine
>
>
> Christine Labno, Ph.D.
> Asst. Technical Director
> Light Microscopy Core
> University of Chicago
> Office of Shared Research Facilities
> KCBD 1250 900 E. 57th St.
> [phone] (phone)
> Please consider the environment before printing this email.
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of Jacob
> Keller [[hidden email]]
> Sent: Thursday, March 21, 2013 4:50 PM
> To: [hidden email]
> Subject: Measuring only intensities above threshold in stack
>
> Dear List,
>
> is there a simple way to measure/output only those intensities (or the area
> and mean thereof) in each image in a stack which are above a given
> threshold? I can do the thresholding, which changes for every image but is
> based on the stack histogram, but then I can't output the intensities of
> the above-threshold areas, which are changing and moving across the stack.
> I feel that there must be a pull-down option for this, but cannot find
> it...
>
> Any help would be appreciated,
>
> Jacob
>
> --
> *******************************************
>
> Jacob Pearson Keller, PhD
>
> Looger Lab/HHMI Janelia Farms Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> email: [hidden email]
>
> *******************************************
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
*******************************************

Jacob Pearson Keller, PhD

Looger Lab/HHMI Janelia Farms Research Campus

19700 Helix Dr, Ashburn, VA 20147

email: [hidden email]

*******************************************

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html