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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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