Zeiss ZVI file format support development for OpenSlide

[Yves Sucaet]

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_______________________________________________
openslide-users mailing list
openslide-users at lists.andrew.cmu.edu
https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users


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