[ome-devel] optimised viewer for time laps data

[Kai Schleicher]

Hi Curtis,

thanks for your reply and for clarification!
I was using the [2], i.e. the OMERO.insight-ij integration and opened 
the tl data as a virtual stack.

Cheers,
Kai


On 01/20/2017 01:41 PM, Curtis Rueden wrote:
> Hi Kai,
>
> > viewing the images in FIJI when fetched via the FIJI-OMERO-connector
> > using virtual stack.
>
> I am curious: do you mean ImageJ-OMERO [1]? Or the OMERO.insight-ij 
> integration [2]?
>
> Regards,
> Curtis
>
> [1] https://github.com/imagej/imagej-omero
> [2] http://help.openmicroscopy.org/imagej.html
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Jan 20, 2017 at 6:37 AM, Kai Schleicher 
> <kai.schleicher at unibas.ch <mailto:kai.schleicher at unibas.ch>> wrote:
>
>     Hi,
>
>     In our facility we have a couple of users that store large time
>     laps datasets in OMERO.
>     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. ).
>
>     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.
>
>     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.
>
>     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.
>     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.
>
>     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.
>
>     Thanks for your help and cheers,
>     Kai
>
>     -- 
>
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>
>     Kai Schleicher, PhD | Research Associate in Advanced Light
>     Microscopy | Biozentrum, University of Basel | Klingelbergstrasse
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