Open Microscopy Environment

Hi Guys,
Our team has been asked to allow a user to describe additional attributes about an image or set of images when they import them.
Is anyone aware of an out-of-the-box way to add fields, or any idea how this might be done?

Hi,

Since the 4.3 release of OMERO, you can tag images when you import them: Have a look at "Movie 2" on this page: http://www.openmicroscopy.org.uk/site/p ... ro.insight

If you're not familiar with tagging, have a look at this movie: http://cvs.openmicroscopy.org.uk/snapsh ... 2-tags.mov

Does this help, or do you really need an attribute AND a value? If so, you probably need to use the OMERO.editor, although this can't be done at the point of import at the moment.

Will.

Hi Will,
Thanks for the quick response

The way the tagging works is similar to what we are after but it's not quite what we're looking for.

We'd like to be able to allow the scientists to specify things like Project Name (and associated ID), Field of Research Codes (if known), Location image/dataset taken, keywords etc when they import new data. Once the images/dataset is published (identified by using a tag) the metadata and possibly the image will be made discoverable.

Ideally it would be a feature that would allow an administrator to attach or add customised metadata to a single image or a dataset that the scientists would fill out when they import files.

Any ideas?
Or would it be better for us to persue creating an event-driven script?

Cheers,
Heidi

Hi,

The functionality you're looking for is something that we've considered for a while, but only just started to do something about (with the Tagging on Import).

We'll trac this work under this ticket: http://trac.openmicroscopy.org.uk/ome/ticket/1797

For now, some questions that occur:

- When users import, do you want to give them a choice of templates they fill out?
- How complex is the template? E.g. Simple list of attributes (like column headers in a table)? Or "fully featured" like OMERO.editor, with a "type" for each parameter (boolean, String, integer etc), options for some fields, default values, "required" vv optional parameters etc.
- If I'm importing 100 images with 10 fields each, when do I fill these out? E.g. after I hit "Import" (before importing starts), after import is finished (but how to enforce this) or before Import. E.g. Create an Excel table of images (identified by name) and fill out the values, then pick this file on import.

Currently we have 2 ways of adding key-value annotations to images etc. OMERO.tables or OMERO.editor.
OMERO.tables is under development but here's an early demo of "Batch annotation" http://trac.openmicroscopy.org.uk/ome/a ... ns.mov.zip

OMERO.editor movie is http://cvs.openmicroscopy.org.uk/snapsh ... riment.mov

The complexity of the template fields you want determines which of these to use and is the first question to answer in moving this forwards.

Thanks,

Will

Hi Will,
I've been away for a bit, sorry about the slow response.
Great to hear it's not a completely random request, and thanks for opening the ticket.

In regards to your questions:
When users import, do you want to give them a choice of templates they fill out?
If possible this would be great. We had thought of just using a very broard set of fields that would cover all the gaps from all the file types but, (if I understand correctly) if a user could select their template, say one for an AxioVision file import, and or another for a SPOT RT file import that would be much nicer.

Would there be anyway to restrict who has permissions to create a template, so that only adamins can?

How complex is the template?
Fully featured would be great, as there are some fields that are required and others optional, some fields will need to have a set list of options (e.g. checkboxes, radio buttons), and others just open text. A webform like template.
A simple list of attributes isn't really sophisticated enough as we would like to ensure the naming of the fields is consistent and all relevant metadata is captured correctly for the publishing and discoverability component.

Also, we would like to ensure that users importing images HAVE to specify the missing metadata before any import is successful.

If I'm importing 100 images with 10 fields each, when do I fill these out?
Again ideally....
A) If I select multiple images (or a folder? not sure if this is possible?) at once from my local directory then hit 'import' to go to get ready for download to OMERO, a pop-up box would come up and ask for extra metadata to apply to that SET of images (i.e. all images selected will get the same extra metadata added)
B) If I select a single image from my local directory then hit 'import', a pop-up box would come up and ask for the extra metadata to apply to that file.

It would also be good if the files would automatically upload to the appropriate folder/s based on the extra metadata added, such as Proejct name or Chief Investigator.

From my details above, do you have any idea if/when this functionality might be introduced into OMERO?

Thank-you for responding so quickly to my enquiries, oyu've been wonderfully helpful
Cheers,
Heidi

Hi Heidi,

I added your comments to #1797. There was certainly a lot of interest in exactly this functionality at the uses' meeting in Paris this year. However, the next release, 4.3.2 planned for the Fall won't be able to include this functionality, but it's certainly a candidate for the next major version 4.4.

Would you like to be added to the ticket to see when it gets scheduled?

Cheers,
~Josh

Hi Josh,
That would be great thanks.
Cheers, Heidi