Posted by
Benedikt Nimmervoll on
Aug 20, 2008; 7:38am
URL: http://imagej.273.s1.nabble.com/ImageJ-opens-first-frame-in-lossless-compressed-Metamorph-stk-files-only-tp3695350p3695351.html
The new trunk of the Bio-Formats plugin works wonderful, thank you for this
hint Melissa!
I got this log-file when I tried to drag and drop compressed .stk files
using the ImageJ version 1.41j (without using the Bio-Formats plugin):
"java.lang.ArrayIndexOutOfBoundsException: -1" Maybe this is of any help
for future bug-fixing. For now I am very happy with the Bio-Formats
plugin.
Best regards,
Benedikt
" Hi Benedikt and Wayne,
The latest trunk build of the Bio-Formats plugin for ImageJ (available
at
http://loci.wisc.edu/ome/formats-download.html) is able to open this
compressed STK file. Thank you both very much for providing the
information
necessary to get this file working in Bio-Formats.
Regards,
-Melissa
On Sun, Aug 17, 2008 at 2:02 PM, Rasband Wayne <
[hidden email]> wrote:
> On Aug 16, 2008, at 5:16 AM, Benedikt Nimmervoll wrote:
>
> Hi!
>> Since I am usually doing voluminous timelapse recordings, I have
>> switched on the lossless compression in Metamorph (which is the
software
>> used on the imaging computer). This sadly leads ImageJ to read the
>> first frame of the recording only. Pushing "/" opens the reslice
menu. I
>> am currently using ImageJ 1.41j.
>> A sample is provided on
http://www.megaupload.com/?d=47JYI4SB (sorry
for
>> the inconvenience using a public filesharer, my university does not
>> provide ftp-space). If the stream works, a number of dots should
>> disappear after about 20 seconds and general bleaching occurs over
the
>> whole timelapse.
>>
>
> The Bio_formats plugin should be able to open LZW-compressed Metamorph
STK
> files but it throws an exception when I try to open this sample. The
> TiffDecoder in ImageJ cannot easily be modified to handle formats like
STK
> that are derived from the TIFF standard but the Bio-formats plugin is
> designed to handle such formats. Here is the exception thrown by the
> Bio-Formats plugin:
>
> loci.formats.FormatException: Sorry, old LZW codes not supported
> at loci.formats.codec.LZWCodec.decompress(LZWCodec.java:152)
> at loci.formats.TiffTools.uncompress(TiffTools.java:1729)
> at loci.formats.TiffTools.getSamples(TiffTools.java:1382)
> at
loci.formats.in.BaseTiffReader.openBytes(BaseTiffReader.java:173)
> at
loci.formats.in.MetamorphReader.openBytes(MetamorphReader.java:126)
> at
loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:140)
> at
loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:113)
> at
loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:98)
> at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:177)
> at loci.plugins.Util.openProcessor(Util.java:106)
> at loci.plugins.Importer.run(Importer.java:473)
> at loci.plugins.LociImporter.run(LociImporter.java:74)
> at ij.IJ.runUserPlugIn(IJ.java:173)
> at ij.IJ.runPlugIn(IJ.java:139)
> at ij.Executer.runCommand(Executer.java:104)
> at ij.Executer.run(Executer.java:58)
> at java.lang.Thread.run(Thread.java:613)
>
> -wayne
>
>
>
> Would be great if this problem could be fixed!
>>
>> Please tell me if I can provide any further information!
>>
>> Benedikt Nimmervoll
>>
>> Mag. Benedikt Nimmervoll
>> Department of Physiology and Medical Physics
>> Innsbruck Medical University
>> Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria
>> phone.: +43 512 9003-70856
>>
>"
--
Mag. Benedikt Nimmervoll
Department of Physiology and Medical Physics
Innsbruck Medical University
Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria
phone.: +43 512 9003-70856
email:
[hidden email]