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Approved-By: [log in to unmask]
References: <1218878173.6722.18.camel@beneedict-laptop>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Message-ID:  <[log in to unmask]>
Date:         Sun, 17 Aug 2008 15:02:29 -0400
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Rasband Wayne <[log in to unmask]>
Subject:      Re: ImageJ opens first frame in lossless compressed Metamorph
              .stk files only
Comments: cc: Curtis Rueden <[log in to unmask]>
In-Reply-To:  <1218878173.6722.18.camel@beneedict-laptop>

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

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