measuring the running width of a kymograph 'object'

[TimFeinstein]

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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[jerie]

Hello Tim,

<quote author="TimFeinstein">
... That would require measuring the horizontal dimension of the inner thresholded 'object' in the attached
kymograph...

please find my suggestion here:151130_4Timothy_Feinstein_01bet.ijm

Cheers, Jens

[Cammer, Michael]

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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[TimFeinstein]

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
>
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>------------------------------------------------------------
>This email message, including any attachments, is for the sole use of the
>intended recipient(s) and may contain information that is proprietary,
>confidential, and exempt from disclosure under applicable law. Any
>unauthorized review, use, disclosure, or distribution is prohibited. If
>you have received this email in error please notify the sender by return
>email and delete the original message. Please note, the recipient should
>check this email and any attachments for the presence of viruses. The
>organization accepts no liability for any damage caused by any virus
>transmitted by this email.
>=================================
>
>--
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[TimFeinstein]

Good news, bad news about my quest to jerryrig sonogram-based analysis
with fluorescence data.

We have a plugin for Osirix that allows Simpson biplane analysis of heart
function, but I need to persuade Osirix that my fluorescence data is a
DICOM file.  I tried importing the Tudor DICOM tools plugins, but now I
get a whole lot of errors.  The first error happens when I try using the
Tudor DICOM plugin, and the second happens when I try to use File>Save
AsŠ>Save DICOM.  

As always, any advice appreciated.

Best,


Tim

(1)

 
java.lang.IllegalAccessError: tried to access method
com.jgoodies.forms.layout.RowSpec.<init>(Ljava/lang/String;)V from class
lu.tudor.santec.settings.SettingsPlugin
        at
lu.tudor.santec.settings.SettingsPlugin.addSubPanel(SettingsPlugin.java:326
)
        at
lu.tudor.santec.dicom.gui.DICOMSettingsPlugin.buildPanel(DICOMSettingsPlugi
n.java:312)
        at
lu.tudor.santec.dicom.gui.DICOMSettingsPlugin.init(DICOMSettingsPlugin.java
:280)
        at
lu.tudor.santec.dicom.gui.DICOMSettingsPlugin.<init>(DICOMSettingsPlugin.ja
va:252)
        at
lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:
29)
        at
lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSetting
s.java:42)
        at Send_As_Dicom.run(Send_As_Dicom.java:62)
        at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java
:263)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
        at ij.IJ.runUserPlugIn(IJ.java:214)
        at ij.IJ.runPlugIn(IJ.java:176)
        at ij.Executer.runCommand(Executer.java:132)
        at ij.Executer.run(Executer.java:65)
        at java.lang.Thread.run(Thread.java:695)

(2)

There was a problem with the class
com.jgoodies.forms.builder.ButtonBarBuilder which can be found here:
/Users/tnf8/Desktop/Fiji.app/jars/jgoodies-forms-1.7.2.jar
/Users/tnf8/Desktop/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError:
com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
        at Save_As_Dicom.setup(Save_As_Dicom.java:82)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:48)
        at ij.IJ.runUserPlugIn(IJ.java:214)
        at ij.IJ.runPlugIn(IJ.java:176)
        at ij.Executer.runCommand(Executer.java:132)
        at ij.Executer.run(Executer.java:65)
        at java.lang.Thread.run(Thread.java:695)

java.lang.NoSuchMethodException: Could not find method
com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
There was a problem with the class
com.jgoodies.forms.builder.ButtonBarBuilder which can be found here:
/Users/tnf8/Desktop/Fiji.app/jars/jgoodies-forms-1.7.2.jar
/Users/tnf8/Desktop/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError:
com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
        at Save_As_Dicom.setup(Save_As_Dicom.java:82)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:48)
        at ij.IJ.runUserPlugIn(IJ.java:214)
        at ij.IJ.runPlugIn(IJ.java:176)
        at ij.Executer.runCommand(Executer.java:132)
        at ij.Executer.run(Executer.java:65)
        at java.lang.Thread.run(Thread.java:695)

        at Save_As_Dicom.setup(Save_As_Dicom.java:82)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:48)
        at ij.IJ.runUserPlugIn(IJ.java:214)
        at ij.IJ.runPlugIn(IJ.java:176)
        at ij.Executer.runCommand(Executer.java:132)
        at ij.Executer.run(Executer.java:65)
        at java.lang.Thread.run(Thread.java:695)
run: DICOM_Manager
run: Send_As_Dicom Url:



 

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





On 12/1/15, 12:55 PM, "ImageJ Interest Group on behalf of Feinstein,
Timothy N" <[hidden email] on behalf of [hidden email]> wrote:

>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
>>
>>
>>--
>>ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>------------------------------------------------------------
>>This email message, including any attachments, is for the sole use of the
>>intended recipient(s) and may contain information that is proprietary,
>>confidential, and exempt from disclosure under applicable law. Any
>>unauthorized review, use, disclosure, or distribution is prohibited. If
>>you have received this email in error please notify the sender by return
>>email and delete the original message. Please note, the recipient should
>>check this email and any attachments for the presence of viruses. The
>>organization accepts no liability for any damage caused by any virus
>>transmitted by this email.
>>=================================
>>
>>--
>>ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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