Open Microscopy Environment

I'm very new to OMERO and I'm doing some research work to see if it will fit into a project that has been handed down to me.

I have the server and the web server running and am able to run the Java WebStart app. I only have one .ndpi sample image. When I try to upload that, OMERO.importer simply says "analyzing'. I've left it there for 45 minutes and it still says "analyzing" so I just killed the process.

On the server-side, I made sure numpy and PIL was installed, if that is any help. I can't seem to find any logs (either local or on the server) that gives me any errors.

Can anyone give me any pointers on how to track this down?

.ndpi support in Bio-Formats/OMERO is known to be poor at best. Only images smaller than 65500 x 65500 are supported, and even those are known to take a very long time to read.

We are actively working on this issue, as documented in this ticket:

http://trac.openmicroscopy.org.uk/ome/ticket/5092

If you wish to receive an automated email each time that ticket is updated, please let us know.

Regards,
-Melissa

Grr . . . why make your own work-around when you are breaking the standard? No sense complaining to you, it's not your fault.

I don't know what the max dimensions are of this image. OMERO seems to find all the JPEG layers. I'm trying to import it again, and will let it run all day if I have to. I'm also trying to find images in another formats since ndpi is such a problem child.

For the record -- it took about 3 hours to import the first layer before the Importer ran out of Heap space. I could see the first layer in the view, though, so that is progress! I tweaked the Heap size to 1024MB in the JNLP file and am trying it again.