Former OMERO help site

Hi OME team,
I understand that the OMERO help pages are moving or have moved to omero-guides on readthedocs.io. However, quite a bit of help on the old pages hasn’t moved yet (or maybe I just can’t find it). Are the old help pages still accessible? Everything I tried redirects to omero-guides.
What I was specifically looking for was the documentation on applying metadata tables to plates/screens using the Populate_Metadata.py script.
Thanks,
Damir

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Hi Damir
Thank you very much for your feedback. Indeed, the help pages are gone, and you cannot access them anymore. The majority of the help links are redirected to omero-guides as you noticed.
The reason for this move is that we needed to “modernize” the help both in content and environment. The help was very OMERO.insight-centric, which is not the line OME Team is pursuing now, with OMERO.web being the main client. The environment which help was deployed on was not ideal either, for example missing a search function, and it was much harder to update and deploy for us.
Sorry to break your workflow, but, the good news is:
The content you are looking for is indeed in the omero-guides, namely on

The easiest way to find it is:

  1. Find the top level of omero-guides on https://omero-guides.readthedocs.io/en/latest/index.html
  2. Use the Search box in top left corner, in your case I was able to search for “populate” and “metadata” (entering both terms into the box with a space between them).
  3. This brought me to https://omero-guides.readthedocs.io/en/latest/search.html?q=populate+metadata&check_keywords=yes&area=default
  4. Clicking on either the first or second search result will bring you to the content I am mentioning above.
    Nevertheless, the above workflow might have a problem in case you click onto the first link in the search results and realize that this is not what you want and start searching again. Or, in your case, there could have been a problem because the redirect brought you to a subproject in readthedocs and you were not able to search your way up, as the search is not ideal in such situation.

Please let us know if:

  1. The content I am suggesting https://omero-guides.readthedocs.io/projects/upload/en/latest/metadata.html is the one you are looking for (note that imho this content is richer and more up to date, with more examples than the “help” one was, but maybe you are missing explicitly the mention of the plates ? The functionality with regards the plates is analogous to the Project/Dataset/Image hierarchy as described in that omero-guide.
  2. You had experienced any problems with the search in omero-guides ? If so, what exactly did you do and did not find ? What precise link from help you were using (I mean the original help link which you possibly have bookmarked ?)

Sorry for the wordy answer, hopefully it will help you to start using omero-guides more efficiently.
And we are very keen for any feedback on the omero-guides, so thank you for starting this thread.

All the best

Petr

P. S. : @dsudar You might be interested in the new work-in-progress on the populate metadata in the PR https://github.com/ome/omero-metadata/pull/49

Hi Damir

The original page had a mix of knowledge, we are still in the process of rewriting some of it.
In the mean time, you can still access the previous doc as pdf
The old doc is at https://downloads.openmicroscopy.org/help/pdfs/scripts.pdf

For other docs, go to https://downloads.openmicroscopy.org/help/pdfs

Cheers

Jmarie

Hi Petr and Jmarie,
Thanks. That is all very helpful. Yes, I did find the omero-guides for the metadata CLI tool and I myself am quite familiar with that. However most of our users are CLI-naive so I had been showing them the Populate_Metadata script and couldn’t find much about that in the omero-guides while it was explained fairly extensively in the old help (as I can now see again in the PDF, thanks!).

I did notice in the code that that script is now deprecated (is that correct?). Will there be a new one that will have all the nice new capabilities that the new omero-metadata plugin provides?
Cheers,
Damir

Hi Damir

thank you for this

Populate_Metadata script … and couldn’t find much about that in the omero-guides

I suppose you mean the script which you can run using the Graphical User Interface ? This is described in https://omero-guides.readthedocs.io/en/latest/upload/docs/metadata.html - if you start at step 12. there, which goes “Still in OMERO.web, create a new Dataset …” is basically describing just this, up till the very end of this guide.
There is also an example of the layout of the CSV and a downloadable CSV example, which your users can adjust and execute the script exactly as described.
Note that the description of the steps is shown on a Dataset/Image hierarchy rather than a Screen/Well/Plate hierarchy, but the steps are analogous for both.

The possibility of running the script from the GUI on Project/Dataset/Image hierarchies is a newly added feature, which was never mentioned in https://downloads.openmicroscopy.org/help/pdfs/scripts.pdf simply because it did not exist at times when this help doc was written.

The workflow described in the https://downloads.openmicroscopy.org/help/pdfs/scripts.pdf about the necessity to check the checkbox of the uploaded file is also not valid anymore, your users do not need to do any of that. Additionallly, they can run the GUI script even without attaching the csv to the P/D first, the script will allow them to pick the csv later by browsing and selecting the csv from their local machine.

I did notice in the code that that script is now deprecated (is that correct?).

No, not correct. Quite the opposite, the script has been improved on fairly recently, and it is one of our more popular scripts.

Will there be a new one that will have all the nice new capabilities that the new omero-metadata plugin provides?

There is already the script in GUI which does (possibly partially) what you are asking. The GUI script is principally just calling the omer-metadata plugin and re-uses its code. This is the reason for the “Deprecated” warining you found in the codebase https://github.com/ome/omero-scripts/blob/bb8122c8b5c06a3150368657d19989bfe2f66dab/omero/import_scripts/Populate_Metadata.py#L53. Basically, you will have the most recent GUI script if you upgreade your OMERO.server and install the most recent omero-metadata CLI plugin on youir server. The omero-metadata CLI plugin installation steps are described also in https://omero-guides.readthedocs.io/en/latest/upload/docs/metadata.html, in the Setup and the first steps. The GUI script is re-using the code of the omero-metadata plugin - if it finds an outdated omero-metadta plugin or no omero-metadata plugin, it falls back onto the Deprecated warning and prints it into the GUI script dialog when exacuted. Then, it falls back on the old, deprecated code, which does not use the omero-metadata plugin (and thus does not have the nice new features of course).

Of course, all what I list above is valid on the OMERO 5.6.x.

Indeed, it is the help doc which is deprecated and outdated, not the script or plugin itself, and this makes hopefully the reasoning clear why we went away from the help, as the new features were added.

So how would you suggest we improve the omero-guides for the benefit of your users ?

Is it maybe crucial for them to not have the CLI preambel in the https://omero-guides.readthedocs.io/en/latest/upload/docs/metadata.html ? This means maybe a separate chapter which clearly states “this here it is for GUI users only” ?
Is it crucial to have an explicit Screen/Plate/Well example ?
The script s GUI is not different from other scripts as described in https://omero-guides.readthedocs.io/en/latest/scripts/docs/index.html - I would imagine at least a link between the https://omero-guides.readthedocs.io/en/latest/scripts/docs/index.html and https://omero-guides.readthedocs.io/projects/upload/en/latest/metadata.html would be useful, is anything else necessary ?

Thank you again for your feedback. Looking forward to your suggestions.

All the best

Petr

Hi Petr,

Thanks for the detailed response and glad to see the Populate_Metadata.py script with its GUI is alive and well. As for the omero-guides documentation, indeed that page mentions the script but the way it is introduced, it appears to be just one step in a long sequence of steps that include many CLI calls. So I would suggest that a separate chapter in omero-guides would be useful for all those people that only use the GUI frontends such as omero-web and who don’t have the skills (or even the access due to how their OMERO server is set up) to even consider the CLI.

Yes, I would include a SPW example. It is widely used in our facility and it is particularly useful for people who work with plates. In fact, as an aside, I’m just finishing up a script that reformats (using a modified Dataset_To_Plate.py script) a bunch of TMA core images into a plate container for convenient metadata handling.

Thanks,
Damir

Hi Damir

Thank you for this, very much appreciated.
To help us go ahead with your suggestion with regards to omero-guides improvements, we created https://github.com/ome/omero-guide-upload/issues/12 and will make the changes in due course.

Do you have or will you have the link code of your customized Dataset_To_Plate script available ? It would be a very interesting read for us.

Thanks again for your valuable feedback.

Best

Petr

Hi Petr,
Yes, as soon as I’ve fixed up my TMADataset_To_Plate.py script enough that I’m not too embarrassed about it, I’ll submit it. Should I upload it here?
Cheers,
Damir

Hi Damir,

Should I upload it here?

Yes, please, that would be great.

Thank you