Open Microscopy Environment

Hi,

We are setting a high troughput imaging system that will use COlumbus from Perkin Elmer, which use OMERO as its storage backend. I have followed to the letter the instructions found on the web site to create a mod_python based production server. When I try to get to the server at localhost/webadmin, I get this info on the page:


MOD_PYTHON ERROR

ProcessId: 7028
Interpreter: '127.0.1.1'

ServerName: '127.0.1.1'
DocumentRoot: '/var/www'

URI: '/webadmin/'
Location: '/'
Directory: None
Filename: '/var/www/webadmin'
PathInfo: '/'

Phase: 'PythonHandler'
Handler: 'django.core.handlers.modpython'

Traceback (most recent call last):

File "/usr/lib/python2.6/dist-packages/mod_python/importer.py", line 1537, in HandlerDispatch
default=default_handler, arg=req, silent=hlist.silent)

File "/usr/lib/python2.6/dist-packages/mod_python/importer.py", line 1186, in _process_target
newpath = eval(pathstring)

File "<string>", line 1

['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb] + sys.path

^

SyntaxError: EOL while scanning string literal

I am a PHP person , not a Python person so this info is quite cryptic to me. Anyone can lead me to a solution?

Sylvain

===
Sylvain Foisy, Ph. D.
Montreal Heart Institute
Montreal, Qc
Canada

Code: Select all

['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb] + sys.path;
...


That block is missing a single quote after omeroweb, it should look like this:

Code: Select all

['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb'] + sys.path


Hi,

Wow, that was so simple... The joys of copy-and-paste

Thanks for the help and keep up with this excellent work. BTW, one quickie: could I use OMERO to not only keep info from my high-throughput imaging but also from imaging platforms like gel/film documentation systems?

Best regards

Sylvain

No problem.

foisys wrote:BTW, one quickie: could I use OMERO to not only keep info from my high-throughput imaging but also from imaging platforms like gel/film documentation systems?

Absolutely. Which file formats would you be using? One unfortunate problem with Beta 4.1 is the lack of Li-Cor L2D support, which we hope to fix soon.

Hi,

We have a Bio-Rad suite of imaging devices: GelDoc XR+, GS-800 densitometer, Pharos FX plus and VersaDoc. Most of the users in my group simply take pictures and print but having the possibility of dumping the files in OMERO for later use would be a great bonus for us. In addition, we are building an eLabbook-like system and I could use OMERO as a storage backend!

Best regards

Sylvain

---
Sylvain Foisy, Ph. D.
Montreal Heart Institute
Montreal, Qc
Canada

We try to support as many file formats as we can, so an feedback you have (example files are most useful) would be extremely helpful. You can provide example data here:

http://qa.openmicroscopy.org.uk/qa/upload/

Or via FTP to the Bio-Formats team directly. Whichever works best for you.

Let us know if you have any more issues, comments or suggestions.

Hi,

Sorry if it took a while answering back... What would be the address to send via FTP? I tried the qa interface but the files are not bio-rad .pic files...

Best regards

Sylvain

Hi Sylvain-

We'll send the Bio-Formats FTP info by email.

Cheers,

Jason