Open Microscopy Environment

Hi, we have collected Incell images from a set of 1536 well plates on our robot, but due to a setup issue the well coordinates have been flipped in the output files - ie the XDCE file and the plate file names.

I have been able to import these plates successfully via the importer GUI and I can see the wells in their 'flipped' layout.

Is there a way during the import process (or after the import is done) that I could flip the well coordinates? Can this be solved by some sort of plugin that could hook into the import process?

I could go through the actual XDCE and image files and do the flip myself via a Python script, but was wondering if OME could handle this type of problem.

Thanks,
Rajarshi

There are currently no real extension points within the importer that would allow you to do this. Your options really are limited to modifying the XDCE file with a Python script or similar as you've already suggested or write an OMERO Python script that switches the Well coordinates after import.

Thanks for the suggestions. Are there any examples of OMERO Python scripts that I could work of of?

If you look in the Insight or Web client, run a script Util_Scripts > Dataset_To_Plate, you will see how to create a plate from a series of images.

Demo Movie:
http://cvs.openmicroscopy.org.uk/snapsh ... -4.3.2.mov

You can access the script from the run-script dialog (bottom left of dialog - "View Script") or look at the code:
https://github.com/openmicroscopy/openm ... o_Plate.py


But really I think all you want to do is switch the column and row values on each well.
In fact, the code below almost does what you want:

Code: Select all

import omero.clients
from omero.gateway import BlitzGateway
from omero.rtypes import rint

user = 'root'
pw = 'ome'
host = 'localhost'

conn = BlitzGateway(user, pw, host=host, port=4064)
conn.connect()

pId = 57
plate = conn.getObject("Plate", pId)

wells = []
for well in plate.listChildren():
    c = well.column
    r = well.row
    print r, c
    well._obj.column = rint(r)
    well._obj.row = rint(c)
    wells.append(well._obj)

conn.getUpdateService().saveArray(wells)


The only problem is that the Save action generates a ValidationException since when you try to swap the position of 2 wells, you try to save one of them in position that is already occupied. It is not valid to have two wells in the same position in a Plate!

You may be able to get around this by first saving all the wells to vacant position E.g. column = 100+column, then placing them back in the desired location. I'll try and think of a nicer solution....!

After a bit of discussion, it turns out that the DB will not allow a "nice" way of doing this, due to various constraints etc. Probably the best way to do it is to temporarily save the wells to a new Plate when switching their rows & columns. Then save them back to the original plate.

The complete script for doing this is at https://gist.github.com/3010541

If you want to allow users to run this from the clients, you can put this logic into an OMERO script (see Dataset_To_Plate.py above). If you get Data_Type as "Plate" instead of "Dataset", and use IDs to get the Plate ID, then the clients will auto-populate these when a Plate is selected and you run the script.