.czi --> DICOM or .mrb ???

[Kenneth Sloan-2]

I have a colleague who has .czi images (Zeiss specific).  He can read and process the files in FIJI.

But, he wants to write them out (to feed to other programs) in either DICOM or .mrb format.

His first attempt to use the “DICOM tudor plugin” (his term) failed - he gets unspecified exceptions in a popup).

While I investigate that - are there any good solutions for:

.czi  —> DICOM  , or
.czi  —> .mrb  ???

All clues gratefully rented.

—
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan-2]

Followup.  This looks like an installation problem.  I have FIJI installed.  The Tudor installation instructions said to unpack their .zip file in the “ImageJ directory”.  I don’t have one of those, so…I unpacked it elsewhere and got a “plugins” directory.  That looked simple enough, so I simply moved the contents into the FIJI plugins directory.

That spawned some complaints about duplicates.  But, I pushed forward, just to see what happened.  Predictably, I got the errors at the bottom of this e-mail.

My current question is: given that I have the Tudor .zip file - how do I install it in my existing FIJI implementation?

While I wait for an answer, or other inspiration, I’m going to clean out the Tudor stuff.

Help, please.  Clearly, my FIJI installation skills are minimal to nonexistent.

My next question will probably be: I want “write out as DICOM” - and found “Send AS Dicom” as the closest thing.  I see that what I got
was “Send As Dicom Url”.  That doesn’t look like what I want.  Any clues on how to write an existing stack out in DICOM format?  Please?

==================
run: Send_As_Dicom Url:
There was a problem with the class com.jgoodies.forms.builder.ButtonBarBuilder which can be found here:
/Applications/Fiji.app/jars/jgoodies-forms-1.7.2.jar
/Applications/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
/Applications/Fiji.app/plugins/TudorDICOMLibs/loci_tools.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
        at lu.tudor.santec.settings.SettingsPanel.<init>(SettingsPanel.java:180)
        at lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:28)
        at lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSettings.java:47)
        at Send_As_Dicom.run(Send_As_Dicom.java:63)
        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:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)

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:
/Applications/Fiji.app/jars/jgoodies-forms-1.7.2.jar
/Applications/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
/Applications/Fiji.app/plugins/TudorDICOMLibs/loci_tools.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
        at lu.tudor.santec.settings.SettingsPanel.<init>(SettingsPanel.java:180)
        at lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:28)
        at lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSettings.java:47)
        at Send_As_Dicom.run(Send_As_Dicom.java:63)
        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:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)

        at lu.tudor.santec.settings.SettingsPanel.<init>(SettingsPanel.java:180)
        at lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:28)
        at lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSettings.java:47)
        at Send_As_Dicom.run(Send_As_Dicom.java:63)
        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:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)
==============================
—
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.

> On Mar 22, 2016, at 09:21, Kenneth Sloan <[hidden email]> wrote:
>
>
>
> I have a colleague who has .czi images (Zeiss specific).  He can read and process the files in FIJI.
>
> But, he wants to write them out (to feed to other programs) in either DICOM or .mrb format.
>
> His first attempt to use the “DICOM tudor plugin” (his term) failed - he gets unspecified exceptions in a popup).
>
> While I investigate that - are there any good solutions for:
>
> .czi  —> DICOM  , or
> .czi  —> .mrb  ???
>
> All clues gratefully rented.
>
> —
> Kenneth Sloan
> [hidden email] <mailto:[hidden email]>
> Vision is the art of seeing what is invisible to others.
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi everyone,

For the archives: using the Tudor DICOM Tools in Fiji was also discussed in
another recent thread:
http://imagej.1557.x6.nabble.com/oib-to-DICOM-tp5016100p5016154.html

I invited the authors to create an update site, which would make it _much_
easier for users to install these tools.

While it is possible that some day I will get around to setting up that
update site myself, and/or integrate the Tudor DICOM Tools into core Fiji,
it is very likely I will never have sufficient time. So it would be great
to get help from others here.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Mar 22, 2016 at 2:05 AM, Kenneth Sloan <[hidden email]>
wrote:

> Followup.  This looks like an installation problem.  I have FIJI
> installed.  The Tudor installation instructions said to unpack their .zip
> file in the “ImageJ directory”.  I don’t have one of those, so…I unpacked
> it elsewhere and got a “plugins” directory.  That looked simple enough, so
> I simply moved the contents into the FIJI plugins directory.
>
> That spawned some complaints about duplicates.  But, I pushed forward,
> just to see what happened.  Predictably, I got the errors at the bottom of
> this e-mail.
>
> My current question is: given that I have the Tudor .zip file - how do I
> install it in my existing FIJI implementation?
>
> While I wait for an answer, or other inspiration, I’m going to clean out
> the Tudor stuff.
>
> Help, please.  Clearly, my FIJI installation skills are minimal to
> nonexistent.
>
> My next question will probably be: I want “write out as DICOM” - and found
> “Send AS Dicom” as the closest thing.  I see that what I got
> was “Send As Dicom Url”.  That doesn’t look like what I want.  Any clues
> on how to write an existing stack out in DICOM format?  Please?
>
> ==================
> run: Send_As_Dicom Url:
> There was a problem with the class
> com.jgoodies.forms.builder.ButtonBarBuilder which can be found here:
> /Applications/Fiji.app/jars/jgoodies-forms-1.7.2.jar
> /Applications/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
> /Applications/Fiji.app/plugins/TudorDICOMLibs/loci_tools.jar
>
> WARNING: multiple locations found!
> java.lang.NoSuchMethodError:
> com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
>         at
> lu.tudor.santec.settings.SettingsPanel.<init>(SettingsPanel.java:180)
>         at
> lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:28)
>         at
> lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSettings.java:47)
>         at Send_As_Dicom.run(Send_As_Dicom.java:63)
>         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:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:745)
>
> 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:
> /Applications/Fiji.app/jars/jgoodies-forms-1.7.2.jar
> /Applications/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
> /Applications/Fiji.app/plugins/TudorDICOMLibs/loci_tools.jar
>
> WARNING: multiple locations found!
> java.lang.NoSuchMethodError:
> com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
>         at
> lu.tudor.santec.settings.SettingsPanel.<init>(SettingsPanel.java:180)
>         at
> lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:28)
>         at
> lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSettings.java:47)
>         at Send_As_Dicom.run(Send_As_Dicom.java:63)
>         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:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:745)
>
>         at
> lu.tudor.santec.settings.SettingsPanel.<init>(SettingsPanel.java:180)
>         at
> lu.tudor.santec.dicom.gui.DicomSettings.getSettingPanel(DicomSettings.java:28)
>         at
> lu.tudor.santec.dicom.gui.DicomSettings.getDicomSettingsPlugin(DicomSettings.java:47)
>         at Send_As_Dicom.run(Send_As_Dicom.java:63)
>         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:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:745)
> ==============================
> —
> Kenneth Sloan
> [hidden email] <mailto:[hidden email]>
> Vision is the art of seeing what is invisible to others.
>
> > On Mar 22, 2016, at 09:21, Kenneth Sloan <[hidden email]>
> wrote:
> >
> >
> >
> > I have a colleague who has .czi images (Zeiss specific).  He can read
> and process the files in FIJI.
> >
> > But, he wants to write them out (to feed to other programs) in either
> DICOM or .mrb format.
> >
> > His first attempt to use the “DICOM tudor plugin” (his term) failed - he
> gets unspecified exceptions in a popup).
> >
> > While I investigate that - are there any good solutions for:
> >
> > .czi  —> DICOM  , or
> > .czi  —> .mrb  ???
> >
> > All clues gratefully rented.
> >
> > —
> > Kenneth Sloan
> > [hidden email] <mailto:[hidden email]>
> > Vision is the art of seeing what is invisible to others.
> >
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html