[Insight-developers] TIFF Support of Zeiss Images
Julien Jomier
julien.jomier at kitware.com
Tue Jul 7 15:54:02 EDT 2009
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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>>>>>>>>> _______________________________________________
>>>>>>>>> Powered by www.kitware.com
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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
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>
>
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