Open Microscopy Environment

Hi Folks,

I'm looking for information/documentation on where images are stored in or via OMERO.

And information on how I could test availability of said images when the file system does strange things with them in the back ground... because I need to test how (badly) our archiving system works here for our SAN...

been digging around and can't find the answer - and clearly I don't understand how it currently works...

Worse, I need to do this for the current version of OMERO - 5.1.x - and the version used in Columbus (OMERO 4.4)

I especially need to locate and track large images or image sets within the file structure.

5.1.x

IIUC depending on how one imports the image(s), there is a folder with the original image(s), or the Managed Repository folder that contains the original images. WHat other folders contain image data (i.e. not metadata)? Are the images converted to e.g. OME-TIFF or is that an export thing?

4.4.x

Presumably the image is imported and copied into /OMERO/Pixels/ and hence resides both in the original location and in the /OMERO/OMERO4_4/ tree?

Dear Paul,

No, OMERO servers don't do any automatic conversion to OME-TIFF after import, that is just a popular myth!

http://www.openmicroscopy.org/site/supp ... y-location has some useful information. It all depends on where your data directory (configured by "omero.data.dir") and managed repository (configured by "omero.managed.dir") are. By default these are "/OMERO/" and "/OMERO/ManagedRepository/" respectively.

In the data directory, "Files/" contains OMERO 4 archived file uploads and companion files, "Pixels/" contains OMERO 4 full uncompressed image data and pyramids, and, of course, "Thumbnails/" has the small thumbnail images. OMERO 5 also uses "Pixels/" for storing pyramids for big images in some formats like JPEG where subresolutions are not directly accessible from the image file. The numeric filenames in "Files/" correspond to the IDs of rows in the "originalfile" database table.

OMERO 5 puts all the uploaded image files and companion files into the managed repository in subdirectories named according to the scheme configured by "omero.fs.repo.path". Each fileset -- the files that need to be together to be read correctly by Bio-Formats -- gets its own subdirectory. When the clients view images imported under OMERO 5, the server is using Bio-Formats to read these files on the fly, with various caching for performance.

After an upgrade from OMERO 4 to OMERO 5, the OMERO 4 images largely remain in that original format on the filesystem, they are not converted and moved into the managed repository.

Cheers,

Mark