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Greetings!<br>
<br>
Thanks for quick replies!<br>
<br>
I looked at Philippe's files (btw, can we put them on the Benjamin's
website as examples?), and<br>
they actually have 4 grayscale layers! Plus, I also learned that
colors representing them on the<br>
combined image can be chosen randomly. There is one problem though:
as in the examples I<br>
already have, those images' sizes are not big, only 1388x1040, which
does not allow me to see<br>
how a real full-slide image would be stored. Nevertheless, it's an
important insight into what we<br>
are dealing with in terms of data stored inside the zvi file format.
One question though: what's<br>
up with all those Original_Metadata files? Where did they come from?
Are these files converted<br>
from another format?<br>
<br>
Best regards,<br>
<br>
-Alexandre Kharlamov<br>
<br>
On 07/09/12 15:14, Mailly Philippe wrote:
<blockquote cite="mid:4FFAA0E9.3060007@snv.jussieu.fr" type="cite">
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Hi,<br>
<br>
I have put on my server some zvi files
(sftp://134.157.183.78/Test_zvi; login phm; pass: nsi2004). They
have been acquire on Zeiss Axiovert 200 with apotome, with
multichannel and Z stacks.<br>
I have added the corresponding metadata file.<br>
<br>
<br>
Philippe<br>
<br>
<div class="moz-cite-prefix">Le 09/07/2012 09:44, Yves Sucaet a
écrit :<br>
</div>
<blockquote
cite="mid:OF99391E27.4C195781-ONC1257A36.00285EAB-C1257A36.002A88A7@histogenex.com"
type="cite"><font face="sans-serif" size="2">Hello,</font> <br>
<br>
<font face="sans-serif" size="2">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 face="sans-serif" size="2">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 face="sans-serif" size="2">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 face="sans-serif" size="2">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 face="sans-serif" size="2">Yves</font> <br>
<br>
<br>
<br>
<font color="#5f5f5f" face="sans-serif" size="1">From: </font><font
face="sans-serif" size="1">Alexandre Kharlamov <a
moz-do-not-send="true" class="moz-txt-link-rfc2396E"
href="mailto:kharlamovalexandre@gmail.com"><kharlamovalexandre@gmail.com></a></font>
<br>
<font color="#5f5f5f" face="sans-serif" size="1">To: </font><font
face="sans-serif" size="1"><a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a></font>
<br>
<font color="#5f5f5f" face="sans-serif" size="1">Date: </font><font
face="sans-serif" size="1">08-07-12 19:42</font> <br>
<font color="#5f5f5f" face="sans-serif" size="1">Subject:
</font><font face="sans-serif" size="1">Zeiss ZVI file format
support development for OpenSlide</font> <br>
<font color="#5f5f5f" face="sans-serif" size="1">Sent by:
</font><font face="sans-serif" size="1"><a
moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu">openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu</a></font>
<br>
<hr noshade="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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