Open Microscopy Environment

Hi,

we recently tried OMERO to store screens images from a BD Pathway and a GE InCell 6000. We can import and see the images fine but cannot download the original images. Download and Export as OME-Tiff are grayed out and the only choice I have are Export as JPG, PNG and Tiff. I tried the Export as Tiff but the images are in RGB not the original 16 bits grayscale. Is there a way to download the original images or is there a plan to make it available.

Thanks,
Daniel

Hi Daniel,

download of screen images might be disabled on your server. Can you check the 'omero.policy.binary_access' property in your server configuration? You can view your configuration with 'bin/omero config get --hide-password'

See https://www.openmicroscopy.org/site/sup ... ary_access

Regards,
Dominik

Hi Daniel,

The main issue is that Bio-Fomats or OMERO cannot define which imported file/files should be downloaded for a particular Well or Image. HCS formats are all different and so OMERO will only know that ALL the files for a particular Plate may be required for any Well / Image in that Plate.

Because download of a whole Plate of data for a single Well / Image is not optimal, it is disabled by default in OMERO, although can be enabled by the config that Dominik linked to above.

Hope that helps you to understand the current behaviour.

Regards,

Will.

Thank you for the answers.

We tried to set the configuration as you mentioned but it still doesn't work. The "Download" button is still grayed.
Here is what we have. Did we missed something ?

./omero config set omero.policy.binary_access "+read,+write,+image,+plate"

./omero config get --hide-password

Ice.IPv6=0
omero.data.dir=/opt/OMERO/OMERO.data
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=omero_user
omero.jvmcfg.percent=20
omero.policy.binary_access=+read,+write,+image,+plate
omero.web.application_server=wsgi-tcp
omero.web.scripts_to_ignore=[]
omero.web.server_email=xxxxx@usherbrooke.ca
omero.web.session_cookie_age=86400
omero.web.session_expire_at_browser_close=True

Thank you for your help.
Daniel

Hi Daniel,

I forgot to check what client you're using? I guess it's the Insight client, since it appears that this functionality is not working in Insight (maybe a bug or it's possible that it was never implemented in Insight).

However it is working for me in the web client.
I hope that is of use to you?

If it's also beneficial for you to also have this in Insight, let us know.
I'll create a ticket to address this.

Regards,

Will.

Hi Wills

Thanks for the reply. Yes I was using Insight and, as you mentioned, the functionality is available in the web client. However, I still have another problem. When I click "download" and choose to zip all file for download I get this message for 1 or 2 minutes:
Download Original Files
Preparing zip for download...
Please close this window once the download is complete.

but then I get an error : 504 Gateway Time-out

I tried to find an attachement somewhere (in Insight and in the web server) but could not find any zip file attached to anything.

Yes it would be really nice to have this functionality working in Insight.

Thanks,
Daniel

Hi Daniel,

Unfortunately the web doesn't allow multiple downloads with a single click, so we try to zip the files together "on the fly" but this can easily take too long and the web server times out.

It might be possible to extend the timeout, but that might not get you much further (the zipping of a large amount of data in temp location may cause other issues).
Is it any use to you to download individual files (instead of zipping them) or do you need the complete plate?

We have been discussing issues with downloading from web: https://trello.com/c/FpqCdCfr/42-omero- ... p-location and https://trello.com/c/HXHVwDXg/140-omero ... load-issue.

Regards,

Will.

Hi,

No it is no use to us to download individual files. Most of the time, we have to download the whole plate (hundreds of images) for analysis. As it is a web related problem, does enabling the download function in Insight would be a workaround ?

Thanks,
Daniel

Hi Daniel,

Insight currently doesn't take the 'omero.policy.binary_access' into account, Screen/Plate downloads are generally disabled. That's a bug. Unfortunately it's not possible to fix that for the upcoming 5.2.3 release (very soon), but I try to tackle that for the next release. I think that should work for you then, as Insight doesn't trigger any server-side zipping, just downloads the original files.

Regards,
Dominik

Hi Dominik,

That would be nice! Thanks for everything.

Daniel