imageJ cant read tiff with packbits 32773 compression?

[Daniel James White]

Dear All,

is anyone else having trouble reading TIFF files
  that have packbits (32773) compression ?

I get an error message saying
ImageJ cannot open TIFF files compressed in this fashion (32773)

according to

http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf

packbits should be a base standard form of tiff  compression that all  
tiff readers should be able to handle...?

Is there some technical reason why imageJ cant open tiff with  
packbits compression?
Patents/licenses?
Or is it just a feature thats not there (yet)

is there a way around it in imageJ?

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0) 351 210 2627 (Work phone at MPI-CBG)
+49  (0) 351 210 1078 (Fax MPI-CBG LMF)
[phone] (Finnish mobile, only when I'm in Finland)
http://www.bioimagexd.net
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[Albert Cardona]

Dan,

I think that ij-imageio is the only package that can open tiffs
compressed like that. It's a plugin by Jarek Sacha.

http://ij-plugins.sourceforge.net/plugins/imageio/index.html

Albert



> Dear All,
>
> is anyone else having trouble reading TIFF files
>  that have packbits (32773) compression ?
>
> I get an error message saying
> ImageJ cannot open TIFF files compressed in this fashion (32773)

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Jeffrey B. Woodward]

Have you tried the ImageIO plugin at
http://ij-plugins.sourceforge.net/plugins/imageio/index.html?  It has
been able to open any TIFF that I have come across; however, it has two
hassles:
1) You have to use the Plugins->ImageIO->... menus to open the files
rather than the standard File->Open methods.
2) From a Plugins programming perspective, the FileInfo structure isn't
setup by the ImageIO openers -- thus, for the few plugins that I have
that require access to the underlying file (rather-than/in-addition-to
the rasterized image contents), I am still outta luck!

-Jeff Woodward


Dan White wrote:

> Dear All,
>
> is anyone else having trouble reading TIFF files
>  that have packbits (32773) compression ?
>
> I get an error message saying
> ImageJ cannot open TIFF files compressed in this fashion (32773)
>
> according to
>
> http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf
>
> packbits should be a base standard form of tiff  compression that all
> tiff readers should be able to handle...?
>
> Is there some technical reason why imageJ cant open tiff with packbits
> compression?
> Patents/licenses?
> Or is it just a feature thats not there (yet)
>
> is there a way around it in imageJ?
>
> cheers
>
> Dan
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Processing and Analysis
> Light Microscopy Facility
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> +49  (0) 351 210 2627 (Work phone at MPI-CBG)
> +49  (0) 351 210 1078 (Fax MPI-CBG LMF)
> [phone] (Finnish mobile, only when I'm in Finland)
> http://www.bioimagexd.net
> http://www.chalkie.org.uk
> [hidden email]
> ( [hidden email] )
>

[ctrueden]

Hi Dan,

The next release of Bio-Formats, available some time next week, will
support reading PackBits compressed TIFFs. Or you can use this
pre-release build, available at:

http://skyking.microscopy.wisc.edu/curtis/jar/loci_tools.jar

Cheers,
Curtis

On 8/29/07, Dan White <[hidden email]> wrote:

> Dear All,
>
> is anyone else having trouble reading TIFF files
>   that have packbits (32773) compression ?
>
> I get an error message saying
> ImageJ cannot open TIFF files compressed in this fashion (32773)
>
> according to
>
> http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf
>
> packbits should be a base standard form of tiff  compression that all
> tiff readers should be able to handle...?
>
> Is there some technical reason why imageJ cant open tiff with
> packbits compression?
> Patents/licenses?
> Or is it just a feature thats not there (yet)
>
> is there a way around it in imageJ?
>
> cheers
>
> Dan
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Processing and Analysis
> Light Microscopy Facility
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> +49  (0) 351 210 2627 (Work phone at MPI-CBG)
> +49  (0) 351 210 1078 (Fax MPI-CBG LMF)
> [phone] (Finnish mobile, only when I'm in Finland)
> http://www.bioimagexd.net
> http://www.chalkie.org.uk
> [hidden email]
> ( [hidden email] )
>