Zeiss ZVI file format support development for OpenSlide

Alexandre Kharlamov kharlamovalexandre at gmail.com
Mon Jul 9 13:05:27 EDT 2012


Thanks for quick replies!

I looked at Philippe's files (btw, can we put them on the Benjamin's
website as examples?), and
they actually have 4 grayscale layers! Plus, I also learned that colors
representing them on the
combined image can be chosen randomly. There is one problem though: as
in the examples I
already have, those images' sizes are not big, only 1388x1040, which
does not allow me to see
how a real full-slide image would be stored. Nevertheless, it's an
important insight into what we
are dealing with in terms of data stored inside the zvi file format. One
question though: what's
up with all those Original_Metadata files? Where did they come from? Are
these files converted
from another format?

Best regards,

-Alexandre Kharlamov

On 07/09/12 15:14, Mailly Philippe wrote:
> Hi,
> 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.
> Philippe
> 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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