[Insight-users] ZEISS Microscopy image file support

[Qian Cheng]

  Hi Gaëtan and Mike,
You really gave some very useful infromation to me, I would try them 
out. Thanks a lot.
Best,
Cheng Qian
  2010/8/31 15:57, Gaëtan Lehmann :
> Hi,
>
> You can use bioformats, which is a very capable tool to read many 
> microscopy formats.
> A C++ binding has been developed recently, but I'm not sure that it 
> keeps the spacing - there was a problem on some systems IIRC.
>
>   http://www.loci.wisc.edu/software/bio-formats
>   
> http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/Building_ITK_Plugin
>
> We have used bioformats to convert the image to tif, then read the tif 
> with a standard ITK reader. The spacing is passed through the standard 
> output and modified on the read image in ITK. This is all done in 
> python, but should be easily reproduced in C++ in you don't want to 
> use WrapITK.
>
>   http://mima2.jouy.inra.fr/darcs/contrib-itk/bioformats/
>
> It works very well here for both .lsm and .zvi files.
>
> Regards,
>
> Gaëtan
>
>
> Le 31 août 10 à 15:30, Michael Jackson a écrit :
>
>> Not sure about the .zvi but one avenue is to export as a tiff/bmp and 
>> the AxioVision will also export an xml file that contains all the 
>> meta data for the image. Then you need to apply to Zeiss for a 
>> license for the xml format documentation. Then you can write an XML 
>> parser that will parse all the meta data from the xml file.
>>  Yep, long, arduous and a pain but this is what we ended up doing 
>> instead of trying to support .zvi or reverse engineering the format.
>> ___________________________________________________________
>> Mike Jackson                      www.bluequartz.net
>> Principal Software Engineer       mike.jackson at bluequartz.net
>> BlueQuartz Software               Dayton, Ohio
>>
>>
>>
>> On Aug 31, 2010, at 9:22 AM, qianc at ee.ethz.ch wrote:
>>
>>> Dear list,
>>> I have been working on the microscopy image processing recently. Now 
>>> the images I mostly use are taken from a ZEISS 200m Microscope and 
>>> an Axiovision software(professional image processing software coming 
>>> together with the Microscope, every additional module costs 
>>> thousands of dollars).
>>>
>>> The image format for Axiovision is call "ZVI". Although the image 
>>> could be saved (exported)as tiff...or other normal format, I am 
>>> afraid the spatial information will lose. What I would like to do is 
>>> taking the advantage of the ITK to process this image format(.zvi 
>>> file) directly. Does anyone know if ITK supports this format? Or 
>>> some other available plugin for ITK to support it? Any suggestion 
>>> would be appreciated. Thanks!
>>> Best,
>>> Cheng Qian
>>>
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