Zeiss ZVI file format support development for OpenSlide

Mailly Philippe philippe.mailly at snv.jussieu.fr
Mon Jul 9 05:14:17 EDT 2012


I have put on my server some zvi files (sftp://; 
login phm; pass: nsi2004). They have been acquire on Zeiss Axiovert 200 
with apotome, with multichannel and Z stacks.
I have added the corresponding metadata file.


Le 09/07/2012 09:44, Yves Sucaet a écrit :
> Hello,
> I've pointed Alexandre to sample ZVI data, but if any of you have 
> additional files, feel free to share with him of course. I'm working 
> with Benjamin on creating a 'feature-complete' set of test data for 
> MRXS, Leica SCN, and ZVI files that can be shared with all of you.
> Furthermore, I can only confirm what Alexandre is writing here, but 
> I'd still like to take the opportunity to stress the importance of the 
> multiple planes issue:
> The AxioVision ZVI files are particularly suited for fluorescence 
> microscopy; whereby you can have multiple channels (for each 
> fluorochrome). Our Zeiss microscope camera can only obtain images in 
> black/white, but by doing this at different wavelengths, you can store 
> different channels in a single ZVI file and overlay them. Then the 
> focal plan kick in: on top of the different channels, you may record 
> various z-stacks in a ZVI file, and go through them to see at which 
> plane a certain immuno is expressed. This is particularly useful to 
> eliminate false-positives, of course. Finally, it is possible to merge 
> these files into a single image, with additional X- and Y-bars to 
> indicate at which plane a particular component was expressed/excited. 
> The merged files are much smaller than the z-stack files, depending on 
> how many planes you chose to record. But even the merged files still 
> contain multiple channels.
> My point is: I think working with multiple planes and channels is 
> essential once you get to fluorescence microscopy (and it may be in 
> other types as well). I'm not sure how many other file formats support 
> this. ZVI is the only one I know of at this point. IHC 
> (Immunohistochemistry) and FISH is becoming more and more important 
> for molecular pathologists, so OpenSlide could build in some 
> provisions to support these features. I look forward to some 
> suggestions on how this could be implemented in a formal way in 
> OpenSlide. In the mean time, of course, Alexandre can still work on 
> 'merged' ZVI files and figure out how the file format works.
> Yves
> From: Alexandre Kharlamov <kharlamovalexandre at gmail.com>
> To: openslide-users at lists.andrew.cmu.edu
> Date: 08-07-12 19:42
> Subject: Zeiss ZVI file format support development for OpenSlide
> Sent by: 
> openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu
> ------------------------------------------------------------------------
> Greetings, list!
> This is Alexandre Khalrmov. I am going to develop support
> for ZVI file format.
> Please, give me links to sample files that I can download
> and play with. I'm currently looking for a file with a considerable
> width and height, to see how it is stored. My bet is that they
> are split into smaller rectangles, but I need to see which
> meta data is involved, for the images I have now are small
> enough to fit into one chunk. Also, I need small files with
> different pixel formats.
> Hopefully all those files are within 100-200 megabytes size, unless
> bigger size is really necessary to prove a concept.
> Please, also, specify the usage rights for each image. Most
> importantly: can this image be used as an example to put on
> OpenSlide website?
> I will be busy with other things till about Thursday, so, no rush.
> So far, I'm just collecting info. And even after that it won't be too
> late.
> Basically, it's a OLE2 compound document storage format, same as
> the one used for Office 97 documents. The file I had a chance to play
> with has several focus planes, (please correct my terminology here),
> and also each image has 3 channels: one for Hoechst 33342, one for
> Cy3 and one for FITC. Each channel is a separate greyscale image,
> however, inside Zeiss' ZEN software, those images can be viewed
> as blue, red and green channels respectively, or as a colored image
> combining those channels into one. My question is, do I need to
> be able to output those channels separately, or should I only care about
> the resulting full-color image? Is there ever more than 3 stains used?
> Also, I've noticed that this has been mentioned by my colleague 
> /Agelos Pappas:/
> for multiple focus planes images, I think it would be important
> to be able to choose the plane to display. I understand, that would 
> require
> change in the API, but this is an important feature! What's the use of
> all this expensive high-resolution imagery if the object is out of 
> focus or
> totally invisible?
> Big thanks go to /Benjamin Gilbert/ for maintaining such an important 
> project.
> I mean, aren't we all going to benefit from medical research, and the 
> situation
> with all these proprietary image formats for healthcare is just 
> something that
> I can't understand: this is just plain wrong.
> Best regards,
> -Alexandre Kharlamov_______________________________________________
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