<font size=2 face="sans-serif">Hi list,</font>
<br>
<br><font size=2 face="sans-serif">For those of you who are interested
in this, it may be useful to play around with some of the software that
handles these filetypes (and fluorescence imaging in itself). One such
package that anyone can download is AxioVision LE, which is available at
</font><a href=http://www.zeiss.de/axiovision><font size=2 face="sans-serif">http://www.zeiss.de/axiovision</font></a><font size=2 face="sans-serif">.
I've submitted four ZVI sample datasets to Benjamin yesterday. That in
combination with the files from Mailly Philippe should help you get started,
to appreciate what common tasks and operations are performed on these data.</font>
<br>
<br><font size=2 face="sans-serif">Another thought I've had: does the upcoming
DICOM 145 format say anything about this? As this WILL be the standard
in the future (if the evolution in radiology is any guide), it may be desirable
for OpenSlide to model any new functionality after DICOM, if they have
any notes on such functions yet.</font>
<br>
<br><font size=2 face="sans-serif">Just my two cents,</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">Benjamin Gilbert <bgilbert@cs.cmu.edu></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">09-07-12 20:01</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Subject:
</font><font size=1 face="sans-serif">Multiplane and
fluorescence API design</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><tt><font size=2>Hello list,<br>
<br>
Hamamatsu VMS and Zeiss ZVI both support multiplane images, and MIRAX <br>
and ZVI both support fluorescence imaging. Either or both of these
<br>
features would require additions to the OpenSlide API. Consistent
with <br>
the rest of OpenSlide, any additional API should be as simple as <br>
possible but not too much simpler.<br>
<br>
I am interested in any comments on what an API for these features should
<br>
look like. Off the top of my head, the design issues include:<br>
<br>
- For fluorescence images, is it reasonable to return only one channel
<br>
per API call?<br>
<br>
- What principal metadata should be associated with each channel? (Is
<br>
it sufficient to provide a short name such as "Cy3"?) With
each focal <br>
plane?<br>
<br>
- Can we assume that every focal plane and fluorescence channel at a <br>
particular pyramid level has the same pixel dimensions?<br>
<br>
- Should alpha be treated as just one of the channels, or should it be
<br>
returned alongside each channel? MIRAX could conceivably discard
<br>
different tiles in different channels. (I'm not sure whether the
format <br>
actually supports this, however.)<br>
<br>
- Will every channel exist on every focal plane and pyramid level? If
<br>
not, is it sufficient to return fully-transparent alpha for the missing
<br>
channels?<br>
<br>
- Is it critical to support more than 8 bits per channel? This would
<br>
require (non-trivial) additional support from Cairo and pixman.<br>
<br>
- How should existing API behave when confronted with a fluorescence <br>
image? Should openslide_read_region() return the first three <br>
fluorescence channels?<br>
<br>
--Benjamin Gilbert<br>
_______________________________________________<br>
openslide-users mailing list<br>
openslide-users@lists.andrew.cmu.edu<br>
</font></tt><a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users"><tt><font size=2>https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</font></tt></a><tt><font size=2><br>
</font></tt>
<br>
<br>
<HR><BR>WARNING: This e-mail, including any attachments, may contain CONFIDENTIAL INFORMATION, including privileged and/or health information. It is for the sole use of the intended recipients. Any unauthorized copying, disclosure, distribution, reproduction, use or retention of this email or the information in it, is strictly FORBIDDEN. If you are not an intended recipient, please notify the sender immediately (REPLY this e-mail) and permanently DELETE the related e-mail. Please be aware that this email and replies to it may be monitored by the sender's company for quality assurance, policy compliance and/or security purposes.
<br>