[Insight-developers] TIFF Support of Zeiss Images

[Bill Lorensen]

I just ran the large file through TIFFImageIO and produces a Meta file
whose header looks like this:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = 0 0 0
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 3.84502e-07 3.84342e-07 7.5e-07
DimSize = 400 300 399
ElementType = MET_UCHAR
ElementDataFile = foo.raw

Does this look correct?

Bill

On Tue, Jul 7, 2009 at 3:24 PM, Curtis Rueden<ctrueden at wisc.edu> wrote:
> 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:
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>> >> >>>>
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>> >> >>>
>> >> >>>
>> >> >> _______________________________________________
>> >> >> Powered by www.kitware.com
>> >> >>
>> >> >> Visit other Kitware open-source projects at
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>> >> >>
>> >> >> Please keep messages on-topic and check the ITK FAQ at:
>> >> >> http://www.itk.org/Wiki/ITK_FAQ
>> >> >>
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>> >> >
>> >> > --
>> >> > 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
>> >> >
>> >> >
>> >
>> >
>
>