Zeiss ZVI file format support development for OpenSlide

Alexandre Kharlamov kharlamovalexandre at gmail.com
Sun Jul 8 13:40:36 EDT 2012

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

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
/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
I mean, aren't we all going to benefit from medical research, and the
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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