Posted by
TimFeinstein on
Dec 02, 2015; 10:25pm
URL: http://imagej.273.s1.nabble.com/measuring-the-running-width-of-a-kymograph-object-tp5015052p5015105.html
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: (914) 309-3270
>>
>>________________________________________
>>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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