Posted by
Wayne Rasband on
Aug 17, 2008; 7:02pm
URL: http://imagej.273.s1.nabble.com/ImageJ-opens-first-frame-in-lossless-compressed-Metamorph-stk-files-only-tp3695350p3695353.html
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