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<p>Hi Will,</p>
<p>thanks for your detailed reply!</p>
<p>
<blockquote type="cite">The FIJI viewer actually downloads all the
planes locally when you open an image.</blockquote>
I have used the OMERO.insight-ij integration and opened the image
as a virtual stack. This way it was actually quite fast to view
the first frame, but I believe it opens the images only
frame-by-frame, correct? Indeed loading all frames into memory
first is not what I am looking for as this would take very long.</p>
<p>
<blockquote type="cite">I have been considering a web viewer that
loads multiple planes in hand E.g. see <a moz-do-not-send="true"
href="http://codepen.io/will-moore/pen/Beuyc" class="">http://codepen.io/will-moore/pen/Beuyc</a> (mouse
wheel to scroll through Z)</blockquote>
This is brilliant! Already for showing the "orthogonal view", I am
sure this would be appreciated a lot by our users!</p>
<p>One request regarding viewing tl data was that the users wish to
"hop" around in the video, i.e. jump from the first frame directly
~100 frames forward to the middle/end of the tl.<br>
I guess with the approach of loading multiple frames at once this
would still pose a problem if they wish to see a frame very "far"
away.<br>
</p>
<p>
<blockquote type="cite">You could build a python viewer that
behaved similarly to the FIJI viewer, but I’m not sure this
would get you any advantages over using FIJI?</blockquote>
From what I understand I assume it comes down to whats the fastest
way to load an image. As I found the FIJI viewer with virtual
stack to perform faster than the desktop clients viewer I was
wondering if theres further performance improvement possible when
writing a "dedicated tl-viewer". <br>
But I can see from
<a class="moz-txt-link-freetext" href="https://github.com/openmicroscopy/omero-webtest/pull/11">https://github.com/openmicroscopy/omero-webtest/pull/11</a> that you
are already on this :)</p>
<p>Thanks again and cheers,<br>
Kai<br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 01/20/2017 02:24 PM, William Moore
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:%3C5DCC62FA-8A8C-4D80-A8E4-22E06FE22707@dundee.ac.uk%3E"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Kai,
<div class=""><br class="">
</div>
<div class=""> The reason for the different speeds of the viewers
is because they access the data in different ways.</div>
<div class=""><br class="">
</div>
<div class="">Webclient is slowest since it only loads a single
plane at a time and for each plane we have to initialise the
rendering engine (open the image file etc).</div>
<div class="">Insight is faster because it keeps the rendering
engine open while you’re viewing the image so it doesn’t have to
open the file each time you request a plane.</div>
<div class="">However, you are still reading a plane at a time
from the server.</div>
<div class="">The FIJI viewer actually downloads all the planes
locally when you open an image. This means it takes longer to
open the image but then you</div>
<div class="">have all the data in hand, so there’s nothing to
load remotely when you scroll through planes.</div>
<div class=""><br class="">
</div>
<div class="">I have been considering a web viewer that loads
multiple planes in hand E.g. see <a moz-do-not-send="true"
href="http://codepen.io/will-moore/pen/Beuyc" class="">http://codepen.io/will-moore/pen/Beuyc</a> (mouse
wheel to scroll through Z)</div>
<div class="">but you’d have to reload all the rendered planes
from OMERO when you change the rendering settings.</div>
<div class="">Also it becomes unviable to load all planes for
larger images.</div>
<div class=""><br class="">
</div>
<div class="">Ah - just found that this same question (with
similar response) can be found at <a moz-do-not-send="true"
href="https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8079"
class="">https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8079</a></div>
<div class=""><br class="">
</div>
<div class="">You could build a python viewer that behaved
similarly to the FIJI viewer, but I’m not sure this would get
you any advantages over using FIJI?</div>
<div class=""><br class="">
</div>
<div class="">We’ll discuss “potential for improving the
situation” and let you know if there’s any positive news.</div>
<div class=""><br class="">
</div>
<div class=""> Regards,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 20 Jan 2017, at 12:37, Kai Schleicher <<a
moz-do-not-send="true"
href="mailto:kai.schleicher@unibas.ch" class=""><a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a></a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi,<br class="">
<br class="">
In our facility we have a couple of users that store large
time laps datasets in OMERO.<br class="">
Viewing these, i.e. replaying and scrolling around in
these tl files is however problematic when using the OMERO
viewer, with several seconds long pauses when jumping
between frames depending on the size of the images (e.g.
).<br class="">
<br class="">
I did however notice that there are performance difference
depending on the viewer that is used. Here I have tested
the web-viewer, desctop-client-viewer and viewing the
images in FIJI when fetched via the FIJI-OMERO-connector
using virtual stack.<br class="">
<br class="">
While the desktop-clients-viewer performs about 40% faster
than the web-client, the FIJI-OMERO connector provided
another increase of about 40% in replay speed compared to
the desktop-client.<br class="">
<br class="">
While I am aware that these viewers are not meant to be
optimal for tl-data, my tests make me wonder if it would
be possible to write a simple viewer (e.g. in python)
dedicated to only this task and optimise it for speed.<br
class="">
I apologise if this question is very naive (and I am also
_not_ asking you to write a new viewer :)), but I was
simply wondering if there is any potential improving the
situation for our users by this approach.<br class="">
<br class="">
Of course, if you happen to know other factors that also
influence the speed at which tl data is replayed, e.g. the
file format used, let me know and I'd be happy to try them
outI'd be happy to know and try them out.<br class="">
<br class="">
Thanks for your help and cheers,<br class="">
Kai<br class="">
<br class="">
-- <br class="">
<br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class="">Please note my NEW
PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22
50 (central)<<<br class="">
</blockquote>
</blockquote>
Kai Schleicher, PhD | Research Associate in Advanced Light
Microscopy | Biozentrum, University of Basel |
Klingelbergstrasse 50/70 | CH-4056 Basel |<br class="">
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50
(central) | <a moz-do-not-send="true"
href="mailto:kai.schleicher@unibas.ch" class="">
kai.schleicher@unibas.ch</a> | <a
moz-do-not-send="true"
href="http://www.biozentrum.unibas.ch" class="">
<a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a></a> | <a
moz-do-not-send="true"
href="http://www.microscopynetwork.unibas.ch" class="">
<a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch">www.microscopynetwork.unibas.ch</a></a><br class="">
<br class="">
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class="">
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</blockquote>
</div>
<br class="">
</div>
<br>
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registered Scottish Charity, No: SC015096</span>
</blockquote>
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