Open Microscopy Environment

not sure if I should be directing this to a bioformats-specific forum... but here goes:

I'm struggling to get DeltaT info for each timepoint in a timelapse, for an image stored on an OMERO server using the python bindings for omero, python-omero v5.4.10. From what I've been able to find in the documentation, it seems like it should be an attribute of image.pixels.plane ... but after loading an image (

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conn.getObject()

) and getting the pixels (

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im.getPrimaryPixels()

) the pixel wrapper object I get has only a getPlane() function that just returns the actual numpy array, but no "getPlaneDeltaT" or similar function, that I've seen referred to elsewhere.

if anyone can provide a basic example of extracting DeltaT info from an image ID on OMERO, using the python bindings, I would be grateful!

for anyone else who stumbles upon this, I was able to find a working example in the example omero scripts on github: https://github.com/openmicroscopy/omero-example-scripts/blob/master/analysis_scripts/Simple_FRAP.py#L108

In this particular example... the query was actually performed in SQL using BlitzGateway.getQueryService()... so maybe this particular bit of metadata hasn't been exposed with the python wrapper yet?

Hi,

it is in the pixel wrapper, but the method is called 'copyPlaneInfo'.

Here's an example:

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from omero.gateway import BlitzGateway

conn = BlitzGateway(USERNAME, PASSWORD, host="HOSTNAME")
conn.connect()

image_id = 123

img = conn.getObject("Image", oid=image_id)
pix = img.getPrimaryPixels()
for plane_info in pix.copyPlaneInfo():
    print "Plane ID: %d , Channel: %d, deltaT: %f, exposureTime: %f" %\
          (plane_info.getId(), plane_info.theC, plane_info.getDeltaT(),
           plane_info.getExposureTime())

conn.close()


Regards,
Dominik

Thanks very much!