[Insight-developers] TIFF Support of Zeiss Images
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Tue Jul 7 17:27:48 EDT 2009
It seems that things have been improved since my last check - I
thought it was during the last OME user meeting... I must have done
something wrong.
I can't see what may have improved the situation with images with
several channels, but well, it opens the image. Great!
However, I'm not getting the expected content here with Curtis' image,
nor with http://voxel.jouy.inra.fr/blastocyste.lsm . The first slice
is ok, the others are black. My ITK build is a bit old ('itk version
3.13.0, itk source $Revision: 1.3032 $, $Date: 2009-05-14 02:00:19 $
(GMT)') on my laptop - maybe it can explain that problem.
Also, when opening the image with a VectorImage, I get 3 channels
instead of 2. Do you have the same behavior?
For the test image, if needed, we can produce a small lsm image for
ITK with no copyright risk.
Gaëtan
Le 7 juil. 09 à 21:54, Julien Jomier a écrit :
> Hi Bill,
>
> Mathieu Malaterre posted one in the Insight Journal a couple years
> ago:
>
> http://hdl.handle.net/1926/139
>
> maybe that would do the trick. Otherwise let me know and I'll try to
> find another one.
>
> Julien
>
> Bill Lorensen 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
>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>
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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
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>>
--
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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