[Insight-developers] TIFF Support of Zeiss Images

Curtis Rueden ctrueden at wisc.edu
Tue Jul 7 15:44:34 EDT 2009 

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
> >> >> >>>> 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
> >> >> >
> >> >> >
> >> >
> >> >
> >
> >
>
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