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Reading error with deconvolution

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Reading error with deconvolution

Christopher Albin-Brooks
Greetings,

My lab is looking to get into using imagej (specifically for vamping) and
are excited for the possibilities it can provide us, but we seem to
encounter an error/exception when we try to open deconvoluted image-stacks.
We can view our images fine prior to deconvolution and can use vamping for
them, but we're hoping to try to run through the vamping process with a 3D
convolution using AutoQuant.

The error/exception reads as:

java.lang.ClassCastException: [F cannot be cast to [S
at Ics_Opener$IcsImport.OpenIcs(Ics_Opener.java:378)
at Ics_Opener.open(Ics_Opener.java:91)
at Ics_Opener.run(Ics_Opener.java:34)
at ij.IJ.runUserPlugIn(IJ.java:183)
at ij.IJ.runPlugIn(IJ.java:150)
at ij.IJ.runPlugIn(IJ.java:139)
at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:278)
at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:140)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:242)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
at ij.IJ.runUserPlugIn(IJ.java:183)
at ij.IJ.runPlugIn(IJ.java:150)
at ij.IJ.runPlugIn(IJ.java:139)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:410)
at ij.io.Opener.openImage(Opener.java:287)
at ij.plugin.FolderOpener.run(FolderOpener.java:175)
at ij.IJ.runPlugIn(IJ.java:156)
at ij.Executer.runCommand(Executer.java:127)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:619)

Thank you very much for your time.

-Chris

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Re: Reading error with deconvolution

ctrueden
Hi Chris,

> java.lang.ClassCastException: [F cannot be cast to [S

This error probably means the plugin was expecting a 16-bit integer image
plane, but encountered a 32-bit floating point one.

Did you try opening your ICS data with the Bio-Formats Importer plugin?
(File > Import > Bio-Formats)

Bio-Formats is included with the Fiji distribution of ImageJ (
http://fiji.sc/).

Regards,
Curtis


On Mon, Feb 11, 2013 at 3:06 PM, Christopher Albin-Brooks <
[hidden email]> wrote:

> Greetings,
>
> My lab is looking to get into using imagej (specifically for vamping) and
> are excited for the possibilities it can provide us, but we seem to
> encounter an error/exception when we try to open deconvoluted image-stacks.
> We can view our images fine prior to deconvolution and can use vamping for
> them, but we're hoping to try to run through the vamping process with a 3D
> convolution using AutoQuant.
>
> The error/exception reads as:
>
> java.lang.ClassCastException: [F cannot be cast to [S
> at Ics_Opener$IcsImport.OpenIcs(Ics_Opener.java:378)
> at Ics_Opener.open(Ics_Opener.java:91)
> at Ics_Opener.run(Ics_Opener.java:34)
> at ij.IJ.runUserPlugIn(IJ.java:183)
> at ij.IJ.runPlugIn(IJ.java:150)
> at ij.IJ.runPlugIn(IJ.java:139)
> at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:278)
> at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:140)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:242)
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
> at ij.IJ.runUserPlugIn(IJ.java:183)
> at ij.IJ.runPlugIn(IJ.java:150)
> at ij.IJ.runPlugIn(IJ.java:139)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:410)
> at ij.io.Opener.openImage(Opener.java:287)
> at ij.plugin.FolderOpener.run(FolderOpener.java:175)
> at ij.IJ.runPlugIn(IJ.java:156)
> at ij.Executer.runCommand(Executer.java:127)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:619)
>
> Thank you very much for your time.
>
> -Chris
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Reading error with deconvolution

Christopher Albin-Brooks
Hi Curtis,

I downloaded that plugin and can open the files perfectly now, thank you
very much. However, now I'm having some trouble with the vamping plugin in
trying to run the photos through their algorithm. I'm going to look into
saving files in a 16-bit format.


On Mon, Feb 11, 2013 at 4:38 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Chris,
>
> > java.lang.ClassCastException: [F cannot be cast to [S
>
> This error probably means the plugin was expecting a 16-bit integer image
> plane, but encountered a 32-bit floating point one.
>
> Did you try opening your ICS data with the Bio-Formats Importer plugin?
> (File > Import > Bio-Formats)
>
> Bio-Formats is included with the Fiji distribution of ImageJ (
> http://fiji.sc/).
>
> Regards,
> Curtis
>
>
> On Mon, Feb 11, 2013 at 3:06 PM, Christopher Albin-Brooks <
> [hidden email]> wrote:
>
> > Greetings,
> >
> > My lab is looking to get into using imagej (specifically for vamping) and
> > are excited for the possibilities it can provide us, but we seem to
> > encounter an error/exception when we try to open deconvoluted
> image-stacks.
> > We can view our images fine prior to deconvolution and can use vamping
> for
> > them, but we're hoping to try to run through the vamping process with a
> 3D
> > convolution using AutoQuant.
> >
> > The error/exception reads as:
> >
> > java.lang.ClassCastException: [F cannot be cast to [S
> > at Ics_Opener$IcsImport.OpenIcs(Ics_Opener.java:378)
> > at Ics_Opener.open(Ics_Opener.java:91)
> > at Ics_Opener.run(Ics_Opener.java:34)
> > at ij.IJ.runUserPlugIn(IJ.java:183)
> > at ij.IJ.runPlugIn(IJ.java:150)
> > at ij.IJ.runPlugIn(IJ.java:139)
> > at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:278)
> > at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:140)
> > at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:242)
> > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
> > at ij.IJ.runUserPlugIn(IJ.java:183)
> > at ij.IJ.runPlugIn(IJ.java:150)
> > at ij.IJ.runPlugIn(IJ.java:139)
> > at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:410)
> > at ij.io.Opener.openImage(Opener.java:287)
> > at ij.plugin.FolderOpener.run(FolderOpener.java:175)
> > at ij.IJ.runPlugIn(IJ.java:156)
> > at ij.Executer.runCommand(Executer.java:127)
> > at ij.Executer.run(Executer.java:64)
> > at java.lang.Thread.run(Thread.java:619)
> >
> > Thank you very much for your time.
> >
> > -Chris
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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