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<div>Hi Kai</div>
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<div>The difference between the OMERO.insight and OMERO.insight-ij when viewing an image</div>
<div>is that when the image is opened in OMERO.insight-ij</div>
<div>the plane is retrieved from OMERO using the OmeroReader and rendered in ImageJ i.e.</div>
<div>it does not use the OMERO internal rendering engine.</div>
<div>OMERO.insight will usually render all the active channels i.e. several planes</div>
<div>will be read instead of one at a time usually in ImageJ</div>
<div>This could explain the speed difference you noticed</div>
<div><br>
</div>
<div>As mentioned in a recent blog post</div>
<div>http://blog.openmicroscopy.org/future-plans/community/2016/12/21/omero-5-3/</div>
<div>We are focusing our effort on improving the Web client, that also includes the viewer.</div>
<div>Some changes have already been made to the web architecture to allow,for example, the installation of</div>
<div>dedicated viewers e.g. multivew, general view, figure etc.</div>
<div><br>
</div>
<div>We are also exploring alternative mechanism to load the planes</div>
<div>depending on the history navigation: this will support the "hop" use case mentioned in your e-mail.</div>
<div>Some of the features might be integrated, time alllowing, in the new app viewer https://github.com/ome/omero-iviewer</div>
<div>before its first release.</div>
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<div>Cheers</div>
<div>jmarie</div>
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<span style="font-weight:bold">From: </span>ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk">ome-devel-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Saturday, 21 January 2017 16:34<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-devel] optimised viewer for time laps data<br>
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<p>Hi Will,</p>
<p>thanks for your detailed reply!</p>
<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>
<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>
<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></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>
<p>Thanks again and cheers,<br>
Kai<br>
</p>
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<br>
<div class="moz-cite-prefix">On 01/20/2017 02:24 PM, William Moore (Staff) wrote:<br>
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<blockquote cite="mid:%3C5DCC62FA-8A8C-4D80-A8E4-22E06FE22707@dundee.ac.uk%3E" type="cite">
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="">
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<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>
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<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><a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</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><a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a> |
<a moz-do-not-send="true" href="http://www.microscopynetwork.unibas.ch" class="">
</a><a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch">www.microscopynetwork.unibas.ch</a><br class="">
<br class="">
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span></blockquote>
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