[Insight-developers] TIFF Support of Zeiss Images

Tue Jul 7 15:47:57 EDT 2009

Curtis,

Thanks for the data and verification.

If I don't hear from Julien, I'll check in the small file you provided
and add a test. I assume we can distribute the file with ITK?

Bill

On Tue, Jul 7, 2009 at 3:44 PM, Curtis Rueden<ctrueden at wisc.edu> wrote:
> Hi Bill,
>
>> Does this look correct?
>
> curtis at monk:~$ showinf 2chZT.lsm -nopix -nometa
> Checking file format [Zeiss Laser-Scanning Microscopy]
> Initializing reader
>         Removing thumbnails
>         Reading LSM metadata for series #0
> Initialization took 0.681s
>
> Reading core metadata
> Filename = 2chZT.lsm
> Series count = 1
> Series #0:
>         Image count = 399
>         RGB = true (2)
>         Interleaved = false
>         Indexed = false (true color)
>         Width = 400
>         Height = 300
>         SizeZ = 21
>         SizeT = 19
>         SizeC = 2 (effectively 1)
>         Thumbnail size = 128 x 96
>         Endianness = motorola (big)
>         Dimension order = XYCZT (uncertain)
>         Pixel type = uint8
>         Metadata complete = false
>         Thumbnail series = false
>
> So, the resolution and image counts match what you're getting. Note that the
> data is really 4-dimensional (21 focal planes and 19 time points, with 2
> channels), but the data is likely correct.
>
> -Curtis
>
> On Tue, Jul 7, 2009 at 2:34 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> 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
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>> >> >> >>>>
>> >> >> >>>> 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
>> >> >> >>
>> >> >> >> Follow this link to subscribe/unsubscribe:
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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
>> >> >> >
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>