<font size=2 face="sans-serif">Hello,</font>
<br>
<br><font size=2 face="sans-serif">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.</font>
<br>
<br><font size=2 face="sans-serif">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: </font>
<br>
<br><font size=2 face="sans-serif">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.</font>
<br>
<br><font size=2 face="sans-serif">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.</font>
<br>
<br><font size=2 face="sans-serif">Yves</font>
<br>
<br>
<br>
<br><font size=1 color=#5f5f5f face="sans-serif">From:
</font><font size=1 face="sans-serif">Alexandre Kharlamov
<kharlamovalexandre@gmail.com></font>
<br><font size=1 color=#5f5f5f face="sans-serif">To:
</font><font size=1 face="sans-serif">openslide-users@lists.andrew.cmu.edu</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Date:
</font><font size=1 face="sans-serif">08-07-12 19:42</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Subject:
</font><font size=1 face="sans-serif">Zeiss ZVI file
format support development for OpenSlide</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Sent by:
</font><font size=1 face="sans-serif">openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu</font>
<br>
<hr noshade>
<br>
<br>
<br><font size=3>Greetings, list!<br>
<br>
This is Alexandre Khalrmov. I am going to develop support<br>
for ZVI file format.<br>
<br>
Please, give me links to sample files that I can download<br>
and play with. I'm currently looking for a file with a considerable<br>
width and height, to see how it is stored. My bet is that they<br>
are split into smaller rectangles, but I need to see which<br>
meta data is involved, for the images I have now are small <br>
enough to fit into one chunk. Also, I need small files with<br>
different pixel formats.<br>
<br>
Hopefully all those files are within 100-200 megabytes size, unless<br>
bigger size is really necessary to prove a concept.<br>
<br>
Please, also, specify the usage rights for each image. Most<br>
importantly: can this image be used as an example to put on<br>
OpenSlide website?<br>
<br>
I will be busy with other things till about Thursday, so, no rush.<br>
So far, I'm just collecting info. And even after that it won't be too<br>
late.<br>
<br>
Basically, it's a OLE2 compound document storage format, same as<br>
the one used for Office 97 documents. The file I had a chance to play<br>
with has several focus planes, (please correct my terminology here),<br>
and also each image has 3 channels: one for Hoechst 33342, one for<br>
Cy3 and one for FITC. Each channel is a separate greyscale image,<br>
however, inside Zeiss' ZEN software, those images can be viewed<br>
as blue, red and green channels respectively, or as a colored image<br>
combining those channels into one. My question is, do I need to<br>
be able to output those channels separately, or should I only care about<br>
the resulting full-color image? Is there ever more than 3 stains used?<br>
<br>
Also, I've noticed that this has been mentioned by my colleague <i>Agelos
Pappas:</i><br>
for multiple focus planes images, I think it would be important<br>
to be able to choose the plane to display. I understand, that would require<br>
change in the API, but this is an important feature! What's the use of<br>
all this expensive high-resolution imagery if the object is out of focus
or<br>
totally invisible?<br>
<br>
Big thanks go to <i>Benjamin Gilbert</i> for maintaining such an important
project.<br>
I mean, aren't we all going to benefit from medical research, and the situation<br>
with all these proprietary image formats for healthcare is just something
that<br>
I can't understand: this is just plain wrong.<br>
<br>
Best regards,<br>
<br>
-Alexandre Kharlamov</font><tt><font size=2>_______________________________________________<br>
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