Re: ImageJ opens first frame in lossless compressed Metamorph .stk files only

Posted by Melissa Linkert on Aug 18, 2008; 7:03pm
URL: http://imagej.273.s1.nabble.com/ImageJ-opens-first-frame-in-lossless-compressed-Metamorph-stk-files-only-tp3695350p3695354.html

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.: [phone]
>>
>