[Insight-developers] TIFF Support of Zeiss Images

Curtis Rueden ctrueden at wisc.edu
Tue Jul 7 15:52:54 EDT 2009 

Hi Bill,

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?
>

Yes, my understanding is that those two LSM datasets are samples provided
for trying out with LSM software, for developers to test their LSM
implementations, etc. (We have had the 2chZT.lsm dataset available for
download on our website for several years and Zeiss hasn't complained, at
least.)

-Curtis

On Tue, Jul 7, 2009 at 2:47 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

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