How to Apply Thresholds of One Stack to Another?

[Jacob Keller]

Dear Group,

how does one apply thresholds or selections from one stack to another? I am
trying to use a fluorescence signal at one wavelength to identify which
cells in a field of view are transfected, but cannot figure out how to
apply this over time in a stack. Ideally, this fluorescence channel could
be thresholded for all time points in the long time-lapse dataset (as much
as ~8000 frames), then applied to the other channels.

A related question is how to make moving ROIs over the course of an
experiment? I have seen that there are many programs for tracking cells,
but I have not found one that cares about quantifying the intensity in the
tracked entity. Seems like this task (tracking a set of cells while
quantifying their intensities) should be easy and common enough, but I have
not yet figured it out--can anyone point me in the right direction?

All the best,

Jacob Keller

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

Jacob Pearson Keller, PhD

Looger Lab/HHMI Janelia Farms Research Campus

19700 Helix Dr, Ashburn, VA 20147

email: [hidden email]

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

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[Kota Miura]

Hi Jacob,

see 2.7 Secondary Measurement in

http://cmci.embl.de/documents/ijcourses#macro_programming_in_imagej

It explains how to use object tracking results to do intensity measurements
over time.

Cheers,
Kota


On Tue, Jan 28, 2014 at 4:50 AM, Jacob Keller <
[hidden email]> wrote:

> Dear Group,
>
> how does one apply thresholds or selections from one stack to another? I am
> trying to use a fluorescence signal at one wavelength to identify which
> cells in a field of view are transfected, but cannot figure out how to
> apply this over time in a stack. Ideally, this fluorescence channel could
> be thresholded for all time points in the long time-lapse dataset (as much
> as ~8000 frames), then applied to the other channels.
>
> A related question is how to make moving ROIs over the course of an
> experiment? I have seen that there are many programs for tracking cells,
> but I have not found one that cares about quantifying the intensity in the
> tracked entity. Seems like this task (tracking a set of cells while
> quantifying their intensities) should be easy and common enough, but I have
> not yet figured it out--can anyone point me in the right direction?
>
> All the best,
>
> Jacob Keller
>
> --
> *******************************************
>
> 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
>

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-------------------------------------------------------------*Dr. Kota Miura*

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging,
European Molecular Biology Laboratory
Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel [phone]

Mobile [phone]

Fax [phone]

http://cmci.embl.de
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