Re: Repeating ROI's in a cell

Posted by Jerome Mutterer-3 on Nov 19, 2014; 3:52pm
URL: http://imagej.273.s1.nabble.com/Repeating-ROI-s-in-a-cell-tp5010534p5010544.html

Hi Michelle,
This macro could get you started:
https://gist.github.com/mutterer/035ade419bf9c96475ce

I'm creating a mask with all hexagons, then use the traced selection and
analyze particles with exclude flag to add relevant hexagons to the roi
manager.
From there, you have your hexagons in it, so you can reuse them to go and
measure on whatever image(s).

Sincerely,
Jerome

On 19 November 2014 16:03, George Patterson <[hidden email]> wrote:

> Hi Michelle,
> I have a few questions.
> >Basically, I would hand draw an ROI around a single
> cell.
> Will this be drawn for each time point?  Or will you use the initial cell
> outline for the entire series?
>
> >Then run a macro that would repeat a predefined size hexagon within
> the boundaries of my pre-drawn ROI.  Then each ROI would record the mean
> intensities over 100-200 frames.
> Will the ROIs need to move as the cell moves?  This relates to my first
> question.
>
> >Then I would group that data by intensity
> and duration of the intensity change.
> Just to be clear.  Group by intensity in each frame?  Or total intensity
> over the course of the 100-200 frames?
>
> George
>
> On Tue, Nov 18, 2014 at 5:34 PM, MichelleL <[hidden email]> wrote:
>
> > Hello everyone,
> >
> > I am very new to ImageJ, but have some programming experience in python,
> > and
> > was seeking some advice.  I am trying to quantify the change in intensity
> > of
> > a protein as a cell is migrating.  I would like to create a macro similar
> > to
> > the one in the image.  Basically, I would hand draw an ROI around a
> single
> > cell.  Then run a macro that would repeat a predefined size hexagon
> within
> > the boundaries of my pre-drawn ROI.  Then each ROI would record the mean
> > intensities over 100-200 frames.  Then I would group that data by
> intensity
> > and duration of the intensity change.
> >
> > I am at a complete loss in how to do this.  I could program in the
> hexagon
> > ROI, but how do I loop that ROI around the predefined limits of a cell?
> > Then, how do I get each ROI to record the intensity changes over time?
> >
> > Any help at all would be much appreciated!
> >
> > Thanks,
> >
> > Michelle
> >
> > <http://imagej.1557.x6.nabble.com/file/n5010534/ImageJROI.png>
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/Repeating-ROI-s-in-a-cell-tp5010534.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
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> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
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--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
12, rue du Général Zimmer
67084 Strasbourg Cedex
T 0367155339
www.ibmp.cnrs.fr

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