[Insight-developers] TIFF Support of Zeiss Images

Bill Lorensen bill.lorensen at gmail.com
Wed Jul 8 07:56:36 EDT 2009 

Tom,
Thanks. Yes I have those images from remote sensing.

Bill

On Wed, Jul 8, 2009 at 3:17 AM, Tom
Vercauteren<tom.vercauteren at gmail.com> wrote:
> Hi Bill,
>
> I don't know for lsm but for vanilla tiff, there actually is a handful
> of regression images at libtiff's homepage:
>  http://remotesensing.org/libtiff/images.html
>
> Also as an off-topic side note, it appears that you are monitoring
> code coverage, this is great! Just for your information, you might be
> interested in the following ctest bug (with patch) which basically
> states that some completely uncovered files may remain unreported:
>  http://www.itk.org/Bug/view.php?id=8932
> Not sure how much it might affect ITK's coverage
>
> Regards,
> Tom
>
>
> On Wed, Jul 8, 2009 at 00:14, Bill Lorensen<bill.lorensen at gmail.com> wrote:
>> I have no reason to believe that the image contents will be correct.
>> I'm surprised that they were read without crashing or exceptions. This
>> code has been around in TIFFImageIO for over three years and, as far
>> as I can tell, has never had public testing.
>>
>> I doubt if the problem is an old tiff library. If we do upgrade, I
>> think we should fully test/cover what we have first. Otherwise how
>> will be know if we are fixing problems or creating new ones.
>>
>> I am surprised at a lack of images for regression testing from the
>> tiff community. I don't think there exists a set of images that cover
>> the tiff possibilities. A bit disappointing for such a widely used
>> library.
>>
>> Bill
>>
>>
>> 2009/7/7 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>>>
>>> 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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>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> 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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