Open Microscopy Environment

Sorry if I'm just missing instructions somewhere but I have some basic questions about uploading tile arrays for digital slides:

- I have array of overlapping images (tiles) and list of coordinates of those (in stage navigation units or pixels). How can I upload this tile array to OMERO server for automated stitching / rendering digital slide on server?

- How can I do the same for slides with multiple layers (channels) , each Image tile in this case will have X-Y-Ch coordinates?

- Finally, does upload client use some compression-decompression and format of my image tiles does not affect upload speed or do I have to think about compression and upload speed while choosing image format (e.g. JPEG vs. uncompressed TIFF) ?

Thanks a lot!
Kvit

Hi Kvit,

Unfortunately the functionality you are looking for does not yet exist in OMERO. Currently, the closest to what you want is the "Combine Images" script, for combining multiple single planes across Z, C and T into a multidimensional image. See the Combine Images movie at http://www.openmicroscopy.org/site/supp ... il-scripts.

This functionality needs to be extended to take into account the X and Y positions. Could you give us some idea how the positions would be specified.
E.g,
- Use the image name: image_X256_Y000.tiff

How do the "stage navigation units" relate to pixel sizes?
E.g. 1 stage unit = 0.5 microns, 1 pixel = 0.1 microns?
And how do you store this?

Our proposal for handling tiled images does not handle overlap and hasn't been actively used to date, mostly because OMERO hasn't been able to handle the Big Images from stitching until the last release. We'll review this as we improve our support for tiled images: http://www.ome-xml.org/wiki/TiledImages


The importer does not do compression in order to upload data.
If anything it does the opposite: For some compressed formats that are not supported on the server (we need the raw pixel data) the image is decompressed before upload! However, all the major graphics formats (png, jpeg etc) are now uploaded as they are, then used to build a compressed image "pyramid" on the server.

So, importing JPEG will be quicker to upload than TIFF, although both will take some time to generate an image pyramid on the server. See the movie at: http://www.openmicroscopy.org.uk/site/p ... es-support.

Will.

Probably the best option with the current release is to use some other software to stitch the images together, then import this as a single "Big" image (supports multiple channels etc).

Ticket for supporting tiling better is https://trac.openmicroscopy.org.uk/ome/ticket/6250