Matlab, get pixel size

[Ajaxel]

Hello,
did not find it in the OMERO Matlab language bindings tutorial nor elsewhere...
How to get pixel size information from matlab?
Is it somewhere in
metadataService = session.getMetadataService();

thank you!

[sbesson]

Hi,
assuming you loaded your image using the container service, the image dimensions should be accessible from the pixels using:

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sizeX = image.getPrimaryPixels().getSizeX().getValue()
sizeY = image.getPrimaryPixels().getSizeY().getValue()
..


and the physical pixel sizes using:

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physicalSizeX = image.getPrimaryPixels().getPhysicalSizeX().getValue()
physicalSizeY = image.getPrimaryPixels().getPhysicalSizeY().getValue()
...


Sebastien

[Ajaxel]

thank you it works!
It is getPhysicalSizeX() method!

[bhavna]

Hi,
I just started using the omero server and was able to connect from matlab.
how can we retrive the dimensions of the image and the actual pixel values?
For eg.,
pixels=images(1).getPrimaryPixels();
creates a pointer, but dosnt give the actual pixels ? I am not so familier with java codes..
Are there typical methods mentioned to access the metadata.
Also, how do we retreive the entire metadata in matlab?
Thank You,
Bhavna.

[sbesson]

Hi Bhavna,

Code: Select all

image(1).getPrimaryPixels()

returns a Pixels object, as defined by the OME-XML model. It allows you to access the metadata associated to the Pixels object, e.g.

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image(1).getPrimaryPixels.getSizeX()
image(1).getPrimaryPixels.getSizeY()
image(1).getPrimaryPixels.getSizeZ()
image(1).getPrimaryPixels.getPhysicalSizeX()
...

To access the raw pixel data, you can use the helper methods of the OMERO.matlab toolbox as described in the OMERO developer documentation. For instance to retrieve the plane at coordinates (0,0,0), you can use:

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plane = getPlane(session, image(1), 0, 0, 0);

Sebastien