Can I translate 32-bit ics format to any 16-bit format?

[Dani Díaz de Quijano]

Dear all,

I am a completely newbie biologist trying to use ImageJ, so I apologise for
making so simple questions.

I acquired 3D photos with NIS-Elements (.nd2 extension). They were 16-bit.
I translated them to the ICS format (.ics and .ids extensions)
I deconvolved them with Huygens Essential and, if I well understood, as
energy was relocalized during deconvolution, it shifted to 32-bit.

Now I cannot quantify them back in NIS-Elements becatuse 32-bit images are
not supported.

CAN ImageJ TRANSLATE 32-bit ICS IMAGES TO 16-bit ONES?

When I try to open them at ImageJ, an "Exception" window appears declaring:

java.lang.NullPointerException
    at java.util.Calendar.setTime(Calendar.java:1070)
    at java.text.SimpleDateFormat.format(SimpleDateFormat.java:858)
    at java.text.SimpleDateFormat.format(SimpleDateFormat.java:851)
    at java.text.DateFormat.format(DateFormat.java:316)
    at loci.common.DataTools.formatDate(DataTools.java:814)
    at loci.formats.in.ICSReader.initFile(ICSReader.java:383)
    at loci.formats.FormatReader.setId(FormatReader.java:302)
    at loci.plugins.Importer.run(Importer.java:174)
    at loci.plugins.LociImporter.run(LociImporter.java:72)
    at ij.IJ.runUserPlugIn(IJ.java:176)
    at ij.IJ.runPlugIn(IJ.java:142)
    at ij.IJ.runPlugIn(IJ.java:130)
    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:239)
    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
    at ij.IJ.runUserPlugIn(IJ.java:176)
    at ij.IJ.runPlugIn(IJ.java:142)
    at ij.IJ.runPlugIn(IJ.java:130)
    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:315)
    at ij.io.Opener.openImage(Opener.java:244)
    at ij.io.Opener.openImage(Opener.java:260)
    at ij.io.Opener.open(Opener.java:124)
    at ij.io.Opener.open(Opener.java:63)
    at ij.plugin.Commands.run(Commands.java:23)
    at ij.IJ.runPlugIn(IJ.java:149)
    at ij.Executer.runCommand(Executer.java:104)
    at ij.Executer.run(Executer.java:58)
    at java.lang.Thread.run(Thread.java:619)

What can I do? I have got the feeling I am quite lost...

Thank you very much for your comprehension.


Dani Diaz de Quijano

University of Barcelona

[ctrueden]

This problem is fixed in the latest trunk build of Bio-Formats (available at
http://loci.wisc.edu/ome/formats-download.html).
-Curtis

On Tue, Nov 11, 2008 at 11:11 AM, Dani Díaz de Quijano <
[hidden email]> wrote:

> Dear all,
>
> I am a completely newbie biologist trying to use ImageJ, so I apologise for
> making so simple questions.
>
> I acquired 3D photos with NIS-Elements (.nd2 extension). They were 16-bit.
> I translated them to the ICS format (.ics and .ids extensions)
> I deconvolved them with Huygens Essential and, if I well understood, as
> energy was relocalized during deconvolution, it shifted to 32-bit.
>
> Now I cannot quantify them back in NIS-Elements becatuse 32-bit images are
> not supported.
>
> CAN ImageJ TRANSLATE 32-bit ICS IMAGES TO 16-bit ONES?
>
> When I try to open them at ImageJ, an "Exception" window appears declaring:
>
> java.lang.NullPointerException
>    at java.util.Calendar.setTime(Calendar.java:1070)
>    at java.text.SimpleDateFormat.format(SimpleDateFormat.java:858)
>    at java.text.SimpleDateFormat.format(SimpleDateFormat.java:851)
>    at java.text.DateFormat.format(DateFormat.java:316)
>    at loci.common.DataTools.formatDate(DataTools.java:814)
>    at loci.formats.in.ICSReader.initFile(ICSReader.java:383)
>    at loci.formats.FormatReader.setId(FormatReader.java:302)
>    at loci.plugins.Importer.run(Importer.java:174)
>    at loci.plugins.LociImporter.run(LociImporter.java:72)
>    at ij.IJ.runUserPlugIn(IJ.java:176)
>    at ij.IJ.runPlugIn(IJ.java:142)
>    at ij.IJ.runPlugIn(IJ.java:130)
>    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:239)
>    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>    at ij.IJ.runUserPlugIn(IJ.java:176)
>    at ij.IJ.runPlugIn(IJ.java:142)
>    at ij.IJ.runPlugIn(IJ.java:130)
>    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:315)
>    at ij.io.Opener.openImage(Opener.java:244)
>    at ij.io.Opener.openImage(Opener.java:260)
>    at ij.io.Opener.open(Opener.java:124)
>    at ij.io.Opener.open(Opener.java:63)
>    at ij.plugin.Commands.run(Commands.java:23)
>    at ij.IJ.runPlugIn(IJ.java:149)
>    at ij.Executer.runCommand(Executer.java:104)
>    at ij.Executer.run(Executer.java:58)
>    at java.lang.Thread.run(Thread.java:619)
>
> What can I do? I have got the feeling I am quite lost...
>
> Thank you very much for your comprehension.
>
>
> Dani Diaz de Quijano
>
> University of Barcelona
>