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

[Benedikt Nimmervoll]

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.

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]

[Wayne Rasband]

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]

[Melissa Linkert]

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]
>>
>

[Benedikt Nimmervoll]

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.: [phone]
>>
>"

--
Mag. Benedikt Nimmervoll
Department of Physiology and Medical Physics
Innsbruck Medical University
Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria
phone.: [phone]
email: [hidden email]

[Wayne Rasband]

On Aug 20, 2008, at 3:38 AM, Benedikt Nimmervoll wrote:

> 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.

The ImageJ 1.41k daily build does not display this error message when
opening LZW compressed .stk files but it still only opens the first
image in the stack. You will be even happier with the Bio-Formats
plugin when you discover that you can open files by dragging and
dropping them on the "LOCI Plugins Shortcut Window".

-wayne

>
> 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.: [phone]
>>>
>> "
> --
> Mag. Benedikt Nimmervoll
> Department of Physiology and Medical Physics
> Innsbruck Medical University
> Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria
> phone.: [phone]
> email: [hidden email]
>