Processing OMERO server images with CellProfiler

[PhilippeP]

We have a running OMERO server, no problem in using it, and smooth connection with ImageJ, both ways.
But we have not been able to call and process images stored in OMERO with CellProfiler, which would make things a lot easier for us (high throughput microscopy).
I understand that I should see with the CellProfiler team about that. I did, but it still does not work.
Relevant post is there: http://www.cellprofiler.org/forum/viewt ... =14&t=4307
Does anyone here have any good advice on how to get that running?
Thanx!
Philippe

[emil.rozbicki]

Hi Philippe,

Are the images in your default group? Cell Profiler only allows to access the images that are in the default group if not it will result in errors.

Also to test that everything works fine you could try the following:
1. Fresh open Cell Profiler
2. Drag and drop single OMERO url to Images module omero:iid=ImageId
3. Set No filtering on Filter Images?
4. In Metadata module set Extract metadata to Yes.
5. Set extraction method to: [....] from image file headers
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).
7. If you don't get any errors go back to Images modules and double click the OMERO Image url on the File list this should create a new window with the image - screenshot below.

Image.jpg (148.85 KiB) Viewed 3773 times

It works for me on a Mac, never tried on Windows though.

Cheers,
Emil

[PhilippeP]

Hi Emil,

Thanks for your response that I just found out. I followed your advice, and here is the result:

My test images are in a folder located in my default group. I have access to them through my OMERO server.

1. Fresh open Cell Profiler
OK
2. Drag and drop single OMERO url to Images module omero:iid=ImageId
OK (see attached file "Capture.PNG" which is a screenshot of the simple TestOmero1image.csv file that I used here)
3. Set No filtering on Filter Images?
OK
4. In Metadata module set Extract metadata to Yes.
OK
5. Set extraction method to: [....] from image file headers
OK
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 <lambda>
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

I do not get any login window. I just get the CellProfiler error window.

Any idea?
Philippe

[emil.rozbicki]

Hi Philippe,

I haven't managed to reproduce your error on Mac (no Omero connection Window). I'm getting similar stack trace to the one you reported if I cancel the connection to the Omero sever. It seems that Cell Profiler is not checking whether you are connected or not and just goes on anyway. Have you tried different Cell Profiler versions? I will try to reproduce your error on Windows.

Cheers,
Emil

[PhilippeP]

Hi Emil,
I did try the last stable release of CP, as well as the last available nightly build. Same in both cases...

[emil.rozbicki]

Hi Philippe,

I just tried CellProfiler 2.1.1 (rev 6c2d896) on Windows 8 and all works fine for me. Got the login window, connected to the server and managed to retrieve the image metadata.
Do you have access to another machine? This could possibly tell you if the problem is with you local configuration.

Cheers,
Emil

[PhilippeP]

We are on W7, but I doubt this is the reason why we cannot connect. We will run more test to try to find out where the problem comes from. I don't know if I mentioned, but curiously, we do not have any problem to connect to OMERO through ImageJ on the same machine.
Thank you anyway for testing on W8.
Philippe