Open Microscopy Environment

Hi all,

I'm trying to open .afi and .svs images in matlab using omero server. What I'm getting from "getImages" is a handler like "omero.model.ImageI@608a6df2". Is there a way to open the images using these handler?

Cheers,
Omid

Hi Omid,

the `getImages` method retrieve the Image object in the OME semantics, i.e. containing both the pixel data and the metadata. Assuming you want to accessing the pixel data of the images, you want to use the methods described in http://www.openmicroscopy.org/site/supp ... ata-access.

For instance, the following code will retrieve the first XY plane of an image specified by its ID:

Code: Select all

i = getImages(s, imageId);  # Returns the image object
plane = getPlane(s, i, 0, 0, 0);  # Returns the first plane of the image


See also https://github.com/sbesson/openmicrosco ... taAccess.m for more examples.


Best regards
Sebastien

Thanks a lot!

Omid

sbesson wrote:Hi Omid,

the `getImages` method retrieve the Image object in the OME semantics, i.e. containing both the pixel data and the metadata. Assuming you want to accessing the pixel data of the images, you want to use the methods described in http://www.openmicroscopy.org/site/supp ... ata-access.

For instance, the following code will retrieve the first XY plane of an image specified by its ID:

Code: Select all

i = getImages(s, imageId);  # Returns the image object
plane = getPlane(s, i, 0, 0, 0);  # Returns the first plane of the image


See also https://github.com/sbesson/openmicrosco ... taAccess.m for more examples.


Best regards
Sebastien

You are welcome,

please do not hesitate to let us know if you think either the examples or the documentation are unclear and should either be modified or amended.

Best,
Sebastien