[Insight-developers] TIFF Support of Zeiss Images

[Curtis Rueden]

Hi Bill,

Thanks. The TIFFImageIO read the file. I converted it to png. Does it
> look ok to you?
>

Yes, looks good. That is the first frame. There are multiple pages in the
TIFF, though.

If you want, you can use the Bio-Formats command line tools to convert
microscopy formats to vanilla TIFFs for verification; see:

    http://www.loci.wisc.edu/ome/formats-tools.html

And hopefully soon I can start offering binaries for the Bio-Formats ITK
linkage.

-Curtis

On Tue, Jul 7, 2009 at 2:15 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> Curtis,
>
> Thanks. The TIFFImageIO read the file. I converted it to png. Does it
> look ok to you?
>
> Bill
>
> On Tue, Jul 7, 2009 at 3:06 PM, Curtis Rueden<ctrueden at wisc.edu> wrote:
> > Hi Bill & Gaëtan,
> >
> > Yep, the Zeiss LSM format is quite nasty, with all kinds of edge cases if
> > you want to handle LSMs in the wild. We have been tweaking Bio-Formats to
> > deal with it for years.
> >
> > -Curtis
> >
> > On Tue, Jul 7, 2009 at 2:04 PM, Bill Lorensen <bill.lorensen at gmail.com>
> > wrote:
> >>
> >> The TIFFImageIO does have a bunch of code to handle some sort of tiff
> >> from Zeiss. Julien added it about 3 years ago.
> >>
> >> 2009/7/7 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
> >> >
> >> > Le 7 juil. 09 à 20:56, Bill Lorensen a écrit :
> >> >
> >> >> Curtis,
> >> >>
> >> >> Is it a tiff image? Also, it's huge...
> >> >>
> >> >
> >> > LSM is a kind of tiff. With that name, I guess this is a 2 channels 3d
> +
> >> > time image.
> >> > ITK's LSM reader is not able to read it, so it can be a good input
> image
> >> > for
> >> > a failing test...
> >> >
> >> > Gaëtan
> >> >
> >> >
> >> >> Bill
> >> >>
> >> >> On Tue, Jul 7, 2009 at 2:47 PM, Curtis Rueden<ctrueden at wisc.edu>
> wrote:
> >> >>>
> >> >>> Hi Bill,
> >> >>>
> >> >>> Zeiss has provided one example LSM dataset called 2chZT. You can
> >> >>> download
> >> >>> it
> >> >>> from LOCI's website:
> >> >>>
> >> >>>  http://www.loci.wisc.edu/software/visbio/data/2chZT.zip
> >> >>>
> >> >>> HTH,
> >> >>> Curtis
> >> >>>
> >> >>> On Tue, Jul 7, 2009 at 1:40 PM, Bill Lorensen
> >> >>> <bill.lorensen at gmail.com>
> >> >>> wrote:
> >> >>>>
> >> >>>> Julien,
> >> >>>>
> >> >>>> itkTIFFImageIO supports reading of Zeiss images. I think you added
> >> >>>> this capability a few years ago. We have no example TIFF images to
> >> >>>> exercise this class. Do you have a set of small images to test this
> >> >>>> code? Right now the code coverage for TIFF is 53% (
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>>
> http://www.cdash.org/CDash/viewCoverageFile.php?buildid=372622&fileid=10863748
> >> >>>> ).
> >> >>>>
> >> >>>> Bill
> >> >>>> _______________________________________________
> >> >>>> Powered by www.kitware.com
> >> >>>>
> >> >>>> Visit other Kitware open-source projects at
> >> >>>> http://www.kitware.com/opensource/opensource.html
> >> >>>>
> >> >>>> Please keep messages on-topic and check the ITK FAQ at:
> >> >>>> http://www.itk.org/Wiki/ITK_FAQ
> >> >>>>
> >> >>>> Follow this link to subscribe/unsubscribe:
> >> >>>> http://www.itk.org/mailman/listinfo/insight-developers
> >> >>>
> >> >>>
> >> >> _______________________________________________
> >> >> Powered by www.kitware.com
> >> >>
> >> >> Visit other Kitware open-source projects at
> >> >> http://www.kitware.com/opensource/opensource.html
> >> >>
> >> >> Please keep messages on-topic and check the ITK FAQ at:
> >> >> http://www.itk.org/Wiki/ITK_FAQ
> >> >>
> >> >> Follow this link to subscribe/unsubscribe:
> >> >> http://www.itk.org/mailman/listinfo/insight-developers
> >> >
> >> > --
> >> > Gaëtan Lehmann
> >> > Biologie du Développement et de la Reproduction
> >> > INRA de Jouy-en-Josas (France)
> >> > tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> >> > http://voxel.jouy.inra.fr  http://www.itk.org
> >> > http://www.mandriva.org  http://www.bepo.fr
> >> >
> >> >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/mailman/private/insight-developers/attachments/20090707/d53bd897/attachment.htm>