kymograph to multiple Z profiles

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PJP
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kymograph to multiple Z profiles

PJP
Hi there,
I have a kymograph file and would like to get the z profiles of all the
rows. I know that this can be done by drawing a line, that can be moved
subsequently line-by-line, but this is too tedious (imagine 250 rows). Is
there any way to do it straightforward, i.e., get all the z profiles
simultaneously?
thanks!
Pedro



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Re: kymograph to multiple Z profiles

Krs5
Dear Pedro,

Maybe the code below does what you want

setBatchMode(true);
title = getTitle();
getDimensions(width, height, channels, slices, frames);

for (x=0; x<width; x++){
        selectWindow(title);
        makeLine(x, 0, x, height);
        run("Plot Z-axis Profile");
        if (x==0){
                PlotTitle = getTitle();
        }
        else{
                Pl= getTitle();
                selectWindow(PlotTitle);
                Plot.addFromPlot(Pl, 0);
                Plot.setStyle(x, "black,none,1.0,Line");
                selectWindow(Pl);
                run("Close");
        }
        Plot.setLimitsToFit();

}
setBatchMode(false);

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility

ImageJ workshops 15 and 16 July: https://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/workshops/imagej-workshops-July-2019 


-----Original Message-----
From: PJP <[hidden email]>
Sent: 13 June 2019 18:47
To: [hidden email]
Subject: kymograph to multiple Z profiles

Hi there,
I have a kymograph file and would like to get the z profiles of all the rows. I know that this can be done by drawing a line, that can be moved subsequently line-by-line, but this is too tedious (imagine 250 rows). Is there any way to do it straightforward, i.e., get all the z profiles simultaneously?
thanks!
Pedro



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