Processing OMERO server images with CellProfiler

We are trying to process images directly from our OMERO server with CP (2.1.1 rev 6c2d896, Windows).
I saw the posts on that topic, but could not get it to work nevertheless.
Here is the minimalist .csv (also attached) that we use in our tests. The IDs are correct, and match images in our OMERO server.
URL_Nuc URL_Cyt
omero::iid=357 omero::iid=358
omero::iid=359 omero::iid=360
omero::iid=361 omero::iid=362
omero::iid=363 omero::iid=364
omero::iid=365 omero::iid=366
omero::iid=367 omero::iid=368

Test_OMERO_to_CP.csv (203 Bytes)

We tried both the Input module and the Load module, specifying “No filtering” option. In both cases, we got errors (see attached file)
CP_OMERO_errors.pdf (17.4 KB)

The load module allowed us to establish a valid connection to the server, not the Input module.
When adding an “Identify primary objects” module, and running a test mode, we got a “not an image” error. That image opens fine in OMERO, and is a “regular” .TIFF image, successfully processed by CP when directly loaded from a folder.

What do we do wrong?
I could not find a tutorial or an example pipeline to help in that matter. Is there one?

Any advice would be appreciated!
Thanks,
Philippe

Hi Philippe,

Did you also see this Wiki page on OMERO and CellProfiler? github.com/CellProfiler/CellPro … iler-2.1.0
Please note the last section which details how you need to match the server versions with your .jars in your plugins directory.

Feel free to write back further – I just wanted to make sure you covered all the online help we have already provided.

Thanks,
David

Hi David,
Thank you for pointing me to the blitz.jar, common.jar, ice.jar and model-psql.jar that need to match the versions distributed with the client that works with my server.
I updated these files, but the import still fails through both Import module and LoadData module with the error copied in the attached file.
20150520_OMERO_to_CP_error.pdf (13.2 KB)
I am stuck.
:confused:

Since this post concerns both CP and OMERO, it may be helpful to indicate the post opened on OMERO on the same topic:
openmicroscopy.org/communit … 817#p15817
The last assay ended up with this CP error message (while trying to get an image metadata):

6. Click “Update Metadata” under extraction method in the same panel and not the “Update” button in the bottom panel. This should prompt for OMERO server details and after successful connection will pull the Image metadata from the server or give you an error (e.g. when ImageID does not exists or when it’s not in your default group).
ERROR:
Traceback (most recent call last):
File “cellprofiler\gui\moduleview.pyc”, line 1116, in callback
File “cellprofiler\gui\moduleview.pyc”, line 2012, in __on_do_something
File “cellprofiler\settings.pyc”, line 1944, in on_event_fired
File “cellprofiler\modules\metadata.pyc”, line 484, in
File “cellprofiler\modules\metadata.pyc”, line 860, in do_update_metadata
File “bioformats\formatreader.pyc”, line 953, in get_omexml_metadata
File “bioformats\formatreader.pyc”, line 188, in setId
File “cellprofiler\utilities\jutil.pyc”, line 785, in call
File “cellprofiler\utilities\jutil.pyc”, line 762, in fn
JavaException

Still stuck.
:cry:

Hi,

Sorry about your troubles. Before I file a bug, would you try our latest version, the trunk build here?
http://cellprofiler.org/releases/

It’s possible we have already fixed the culprit bug(s).

Thanks,
David

Hi David,

I tried with the last built (CP2.1.2 (rev 200cfc0) but still no luck.
Here is the message I got:

Traceback (most recent call last):
File “cellprofiler\gui\moduleview.pyc”, line 1124, in callback
File “cellprofiler\gui\moduleview.pyc”, line 2057, in __on_do_something
File “cellprofiler\settings.pyc”, line 1943, in on_event_fired
File “cellprofiler\modules\metadata.pyc”, line 493, in
File “cellprofiler\modules\metadata.pyc”, line 873, in do_update_metadata
File “bioformats\formatreader.pyc”, line 963, in get_omexml_metadata
File “bioformats\formatreader.pyc”, line 664, in init
File “javabridge\jutil.pyc”, line 339, in run_script
JavaException

Hoping this can help sorting out where the problem comes from,
Thanks for the good work.

Philippe

Hi David,
Some more information on ourconnection problem between CP and our OMERO server:

Following a post on the same topic on the OMERO forum, a CP user could import images from OMERO (using CP 2.1.1 (rev 6c2d896) on Windows 8):
openmicroscopy.org/communit … 817#p15868
Just to make sure there is not an install problem on our W7 station, I uninstalled CellProfiler, reinstalled the last trunk build (v2.1.2), updated Java (v8 Update 45), and tried again.
I again got the same exact problem :frowning:

Do you have any information on a putative bug/alternative to connect CP to OMERO?
Philippe

Hi,

Our lead software engineer had this to say:

[quote]The first thing to check is the version they are running on their OMERO server.
They should not try creating a pipeline, they should load a single OMERO URL into the Images file list and try opening it from there.
They should make sure the .jar files in imagej/jars match their server version.[/quote]

Can you try/report these and get back to us? Unfortunately we’re both under deadline pressures here for the next week or two, but hopefully we can diagnose in the meantime.

David

I tried what your lead software engineer suggested:

1- Our OMERO server version is OMERO.web 5.1.1-ice35-b43
2- This is what we tried, as indicated in this thread:
openmicroscopy.org/communit … 821#p15817
3- The blitz.jar, common.jar, ice.jar and model-psql.jar distributed with the client that works with my server (5.1.1-ice35-b43) were copied/pasted into the CellProfiler imagej/jars directory (the corresponding .jar files that were in that folder were already labeled 5.1.1-ice35-b43 following CP install, but were put aside in a backup folder nevertheless to try those of the OMERO client).

Still no luck in opening the image from our OMERO server.

Hi,
Sorry for the delay, but did you have any success? We don’t have a reliable OMERO server here to test with, but I will bring this up again with our software engineers for ideas, thanks.

For reference: https://github.com/CellProfiler/CellProfiler/issues/1706

Hi Phillipe.
I was looking at your post on OME. From the image, it looks like your url is “omero::iid=357”. There are two colons and there should only be one. Can you try “omero:iid=357”?

Thanks,
Lee