[Insight-users] ZEISS Microscopy image file support

[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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-- 
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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