Publishing images using OMERO

[mwoodbri]

We're investigating how we could use OMERO for publishing images. We are aware that others have accomplished this (e.g. JCB, Stowers, Griffiths) and it would be really helpful to discuss the challenges.

Our understanding is that it's relatively straightforward to build a customised, unauthenticated web interface by adding new pages to OMERO.web. Actually, the existing OMERO.web (with a public user account) is almost sufficient, though we do need to add some branding for our institution, prevent anonymous users running scripts, and modify how metadata is displayed (e.g. we need more details regarding research projects, PIs and funding sources).

Some questions:

• It appears that you can't download images in their original format from OMERO.web. Would we be able to add this, or is there a fundamental technical issue why it hasn't been implemented?
  
• We're considering running our 'public' instance of OMERO.web on a separate machine to OMERO itself. Assuming this is straightforward, could there be any major performance issues?
  
• I think that data in OMERO can only be in one group at a time, meaning that publishing data would involve moving it from your personal/lab group to a public group. This is good in the sense that it makes it clear which data is public, but not so good because the public group could become unmanageable, and there is no longer a simple complete catalogue of a lab's data. The alternative is for users to re-upload (i.e. duplicate) the data they wish to make public. This would make it a permanent copy (which is good) but the duplication isn't. Is it currently possible to copy rather than move data? Or does OMERO.fs address these issues?
  
• I'm assuming that 'proper' sharing of images is a better way of publishing than using OMERO.web shares? For example, it seems that you can't link directly to OMERO.web shares, and it would be easy to 'break' one of these shares by deleting the underlying images. But it is a nice, lightweight way of sharing. We have considered implementing a similar thing by just letting people add a tag in OMERO.insight called 'public' to projects, and we then query for this and display the relevant images on our public interface, but this isn't ideal because the web application would need to use the OMERO root password and it would effectively bypass the regular permission checks.

The solution we are favouring at the moment is a standalone, web based publishing tool for internal users, that lets you browse and select projects/datasets and attach a minimum metadata set (organism, project, funding source). It will then assign a persistent identifier and move the images to the public group (and ideally change ownership of the images or make them read-only to protect them, but I don't think this is possible at the moment?). We'll then create our bespoke OMERO.web extensions for public access.

Does this sound like a sensible plan? Any experiences/advice would be much appreciated!

Mark.

[wmoore]

Hi Mark,

Download of Original Images has been supported in web for some time. There should be a Download icon (down arrow) in the right-hand panel (if they've been archived at import). The only limitation is that you can only download a single file at a time, so multi-file imports (E.g. lei + tiffs) are zipped up for download.

I don't know of any performance issues with putting the public web server on a separate machine, but I'm not a sysadmin.

You're correct about data only being in one group at a time. Copying data is something we've discussed but haven't worked on. Can't tell you what the priority is for this at the moment and I'm afraid OMERO.fs won't solve this. We also want to support "Move data from one OMERO server to another" at some point.

You shouldn't need to change ownership of the images to make them read-only. Your 'public-user' (the user who is auto-logged in when displaying public data) should be in a read-only group that also contains the other users and their public data. This means that they'll have read-only access to the public data.

Cheers,

Will.

[mwoodbri]

Thanks Will. By read-only I meant (in this case) that the owner shouldn't be able to (easily) modify a dataset after it has been published, especially if it is related to a publication and has been assigned a persistent identifier. We haven't figured out the best way of achieving this. Please let me know if you have any ideas.

And thanks for pointing out the download button. I forgot to select the archival option. We would like to make it the default but I don't think that's possible (happy to be corrected though).

[kennethgillen]

Hi Mark,

And thanks for pointing out the download button. I forgot to select the archival option. We would like to make it the default but I don't think that's possible (happy to be corrected though).

In fact it is possible to configure the importer to archive by default, but not with the OMERO GUI or the CLI, quoting Jean-Marie: https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=4458&p=9117&hilit=default#p9117

If you want to have the archived flag always on and do not let the user modified the value (from the UI)
you will need to modify the two following values in the importer.xml file. You will find the file in the config folder.

Code: Select all

<entry name="/options/Archived" type="boolean">false</entry>
<!-- if set to true, the user can modify the value -->
<entry name="/options/ArchivedTunable" type="boolean">true</entry>


Hope this helps.

Best,

Kenny

[mwoodbri]

Thanks Kenny. I know about that flag but it's not easy to modify the value when the client is distributed via webstart - presumably we would have to unpack omero.insight.jar, modify the value and the re-sign the jar.

[jmoore]

Mark,

that's likely the case, and you'd need to do that for each new release. If you choose to do that, happy to discuss ways of making it easier!

~Josh.

[i.munro]

Further to this earlier discussion: I wonder if anyone could help us to check our understanding of the current (& near-future) situation regarding the public sharing of data.
Currently we are aware of two possible approaches:
Option 1) Any user can select a subset of their data & create a 'share' using the webApp.
Option 1) has 2 drawbacks from our point of view:
a) The data is completely unstructured (just a 'basket' of images).
b) The public can see the images via the webApp but not get to the data if they wish to re-process it.

Option 2) We set up a second collaborative group, one member of which is public "read-only" user . Any data which we wished to share publicly could then be moved (or copied) into this second group & would become available to anyone via the webApp.

This option 2) means further duplication of data that is copied – with cost implications

Could you please tell us if option 2) is possible and whether there are other, better approaches, of which we are not aware?

Could you also please confirm that it's not currently possible to simply maintain a collaborative group for our normal work and set the permissions of the files in this OMERO database on a file by file basis to allow them to be read by a public user who is a member of this collaborative group.

Best wishes,

Paul

[gus]

Hi Paul

Thanks for your post. In response to your questions:

Could you please tell us if option 2) is possible and whether there are other, better approaches, of which we are not aware?

No this is not possible at the moment. Any data that you want to be shared publicly has to be moved into the Public group of which both you and Public User are members.

Could you also please confirm that it's not currently possible to simply maintain a collaborative group for our normal work and set the permissions of the files in this OMERO database on a file by file basis to allow them to be read by a public user who is a member of this collaborative group.

Correct - this is not possible. Permissions are set at a group level and all data within that group has the same level of permissions.

We are scoping out changes to the Public share functionality, and the scenarios you describe have been requested by other institutions. We are taking a step-wise approach and trying to roll out the easiest improvements as rapidly as we can. However, given the other demands on the team's time at present we cannot give any idea of the time scale for this work.

If you decide to go ahead and do any of it for yourselves, it would be good to go through with you what we have done so far in terms of scoping and see how what you want to do fits in with and can contribute to that.

Many thanks.

Regards
Gus
*******************************
Gus Ferguson
OME UX Team

rkferguson@dundee.ac.uk
www.openmicroscopy.org
*******************************

[i.munro]

Thanks Gus.

Ian

[jwarren]

Hi

We would like to be able to point people at a public url which would enable them to download the original image via webgateway (not in the clients). Has any progress been made on this?

Many thanks

Jonathan.