Open Microscopy Environment

Hi again -
Never mind. I realized that OMERO appears to 'regularize' the dimension order to XYZCT, so that all pixel objects on the server have this order.
I suspect this has a negative impact on performance when retrieving hypercubes.
Best,
Gary

Hi Gary

I'm not sure how relevant this is to your use case but in case it suggests a possible solution for you ...

I had a performance issue with Becker & Hickl .sdt FLIM files via bio-formats as they are not stored in a convenient way for bio-formats to handle - the data is stored such that the decay data is contiguous in memory.

I partly addressed this by buffering the data in the bio-formats reader. When a plane is requested it is returned from the buffer.

At the time it occurred to me that a faster solution would be to add a 'get_FLIM_cube' method to the reader which simply read a whole FLIM 'FOV' x by y by t & returned it.

I didn't do this as it would only make sense if done for all FLIM file types.

Best

Ian

Discussion about hypercube retrieval performance moved to viewtopic.php?f=6&t=7687.