Open Microscopy Environment

Hi,

first of all: Great work with OMERO v5.2., the new UI features are a pleasure to work with.

Some criticism though: Not sure if this has been mentioned before, but both in OMERO.insight v5.2.1 and OMERO.Web, interpolation is turned on per default. Since OMERO is about scientific data, I would propose to change that to a default "off" state. Most users don't know what interpolation is, and interpreting digital image data properly is hard enough without an artificial filtering. Yes, it looks prettier, but that's not what a science tools should be about.

Secondly, and much more gravely: In OMERO.insight, additionally to being interpolated, images are - per default - JPEG compressed with a high rate of compression. This looks terrible and introduces the typical 8x8 JPEG block artifacts (for reference, see: https://www.youtube.com/watch?v=QEzhxP-pdos). JPEG compression might be okay for a quick overview of large amounts of images to save bandwidth, but not in the single image viewer where users want to have an analyzing look on their data.

Thirdly, and this is connected with the last point: Why are the thumbnails still so small in both Web and - especially - Insight? There should be at least an option to change the size. That would also enable users to have a better (and compressed) overview of their data before going into the detailed view. The thumbnails can - of course - be JPEG compressed.

As always, thanks for the good work, and please don't be offended by my comments, they are only meant as as constructive suggestions.

Cheers,

Tristan

PS: It seems interpolation might be off per default in Insight. Not sure if I already saved my rendering settings.

PPS: After some more testing I found that images in OMERO.Web are also rendered with lossy JPEG compression, although much less aggressively. When turning off interpolation and zooming in, it's easily visible, though.

Hi Tristan,

You can configure the default interpolation behaviour in the clients with:

Code: Select all

$ bin/omero config set omero.client.viewer.interpolate_pixels false


See http://www.openmicroscopy.org/site/supp ... ate-pixels

NB: I just checked this and found a bug in web and fixed it https://github.com/openmicroscopy/openm ... /pull/4425 (for 5.2.2), but it's working fine in Insight.

Apologies for that,

Regards,
Will.

Hi Tristan,

Insight takes the initial property for the interpolation from the server, which you can set like Will said in the previous post. If the user changes it, it is preserved in the client side properties. I assume that's why your default changed from enabled to disabled.

You can change the thumbnail size in Insight via the slider on the bottom left of the central panel. However this setting is not preserved. I can add an RFE ticket for that, as it would make sense to store this property. As far as I know, still the default thumbnail size is loaded from the server, but it then gets up or down scaled on the client side according to the setting of the slider.

And thanks for pointing out the issue with JPEG artifacts in full image viewer. I'll have a look into this!

Regards,
Dominik

Hi Will, hi Dominik,

just found the slider to change the thumbnail sizes in both Web and Insight (with your help). I honestly never knew this was possible, not sure how I managed to overlook that. Anyways, sorry for claiming that you couldn't change the thumbnail size. However, preserving the previously chosen size would be a very nice thing to have.

I deactivated the default interpolation now, so this issue should also be gone with the update to v5.2.2.

Now all that remains is the JPEG lossy compression problem.

Cheers,

Tristan

Hi Tristan,

I just checked Insight with respect to the compression issue. The default compression level is based on the server settings (login dialog). If the connection speed is specified as "LAN" no compression will be used by default, with "High" a medium level and with "Low" a high compression level. Does this not work for you?

Regards,
Dominik

I just realized, that was just half-truth. The default compression level is also dependent on the image size. However, I'll address the issue in http://trac.openmicroscopy.org/ome/ticket/13148.

Regards,
Dominik

Hi Dominik,

I had "LAN" selected, and still the compression was set to "High" per default, so apparently for large image sizes, the "LAN" default is entirely overwritten (as you already stated).

Cheers,

Tristan

Hi Tristan,

I fixed the problems in PR https://github.com/openmicroscopy/openm ... /pull/4438 Looks promising it'll go into 5.2.2.

Regards,
Dominik

Hi Tristan,

Sorry for the delay... To answer your question about jpeg compression in web...

By default we use a compression of 0.9 for OMERO's rendering engine (1.0 is uncompressed).

You can experiment with the effects of this compression in your browser by opening the image in a new Tab (right click on the viewer in the Preview tab and "open Image in new tab") adding the compression to the url using 'q' in the query string.

E.g. to remove compression, use ?q=1. I didn't notice any difference from the default but you might?

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webclient/render_image/3455/36/0/?q=1


You will certainly notice some change if you use ?q=0.5 or lower.

Let us know if using no compression helps here.