Re: measuring the running width of a kymograph 'object'

Posted by TimFeinstein on Dec 01, 2015; 5:53pm
URL: http://imagej.273.s1.nabble.com/measuring-the-running-width-of-a-kymograph-object-tp5015052p5015073.html

Hi Michael and Jens,

Thank you so much!  Both of your scripts worked well.

Follow-up question: while we are talking about heart function, has anyone
tried implementing Simpson biplane analysis using ImageJ/Fiji?  This comes
included with modern echo machines but I expect that it will require some
extra work to do it with fluorescence.

Thanks again,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology





On 11/30/15, 9:26 PM, "ImageJ Interest Group on behalf of Cammer, Michael"
<[hidden email] on behalf of [hidden email]> wrote:

>Except for a few stray pixels, this may solve the problem.
>
>
>  // The next two steps fill in the missing pixels on the left side of
>the kymogram
>  makeRectangle(112, 52, 12, 2);
>  run("Set...", "value=0");
>
>  //  Here is the macro which only works if the left and right waves are
>solid
>  //  Counts pixels of value 255 in single pixel high box from top to
>bottom of image
>  w = getWidth();
>  doWand(1,1);
>  run("Set...", "value=0");
>  doWand(w-1, 1);
>  run("Set...", "value=0");
>
>  print("\n" + getTitle());
>  for (i=0; i<getHeight; i++) {
>    makeRectangle(0,i, w,1);
>    getHistogram(values, counts, 256);
>    print(counts[255]);
>  } // for i
>
>
>_________________________________________
>Michael Cammer, Optical Microscopy Specialist
>http://ocs.med.nyu.edu/microscopy
>http://microscopynotes.com/
>Cell: [phone]
>
>________________________________________
>From: ImageJ Interest Group [[hidden email]] on behalf of Feinstein,
>Timothy N [[hidden email]]
>Sent: Monday, November 30, 2015 4:19 PM
>To: [hidden email]
>Subject: measuring the running width of a kymograph 'object'
>
>Hello,
>
>I have a kymograph of a transect through beating heart muscle measured
>using light sheet fluorescence.  I would like to graph 'strain' and
>'strain rate' over time, reflecting the distance and rate of movement of
>the inner wall of the ventricle of interest.  That would require measuring
>the horizontal dimension of the inner thresholded 'object' in the attached
>kymograph from top to bottom in 500 steps.  Does anyone know of a way to
>do this in ImageJ/Fiji?  Apologies if this has come up before and I just
>failed to find it.
>
>Many thanks,
>
>
>Tim
>
>Timothy Feinstein, Ph.D.
>Research Scientist
>University of Pittsburgh Department of Developmental Biology
>
>
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