Open Microscopy Environment

Hello,

I'm probably missing this in the documentation but I was just wondering how I can set the physical pixel size when creating an image from scratch on the server. So, writing an image using 'createImageFromNumpySeq' when a parent image doesn't exist.

Many thanks!

Dan.

Hi Dan,

Here you go...

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from omero.rtypes import rdouble

conn = BlitzGateway('will', 'ome', host="localhost", port=4064)
conn.connect()

# createImage (details not shown)
i = conn.createImageFromNumpySeq (.....)

# reload the image (also reloads pixels)
image = conn.getObject("Image", i.getId())

# Get the BlitzGateway wrapped pixels and unwrap it
pixelsWrapper = image.getPrimaryPixels()
pixels = pixelsWrapper._obj

# Update and save
pixSize = rdouble(1.1)      # in microns

pixels.setPhysicalSizeX( pixSize )
pixels.setPhysicalSizeY( pixSize )

conn.getUpdateService().saveObject(pixels)


Hi Will,

Thanks! Don't know how I missed that.

Cheers,

Dan.

Heads up to anyone reading this now - the setPhysicalSize functions expect a "Length"-type argument instead of an "rdouble", so the line

Code: Select all

pixSize = rdouble(1.1)

should be replaced with

Code: Select all

pixSize = omero.model.LengthI(1.1, omero.model.enums.UnitsLength.MICROMETER)

Reference

Thanks for the heads up.

The docs on this also show the current usage of Units to set pixel size:
https://www.openmicroscopy.org/site/sup ... eate-image

Cheers,

Will.