Conversion of image to ome.tiff before import in OMERO

Proprietary microscopy file formats are very diverse and are for most not suited for the streaming of data over a network, as it is the case when viewing images in OMERO.web.

For this reason, OMERO has to process the images to generate pyramidal resolutions, which helps decrease the amount of data required to transit on the network.

The drawback is that this process takes a consequent amount of resources and is not scalable for OMERO, servicing multiple users at a time.

This is why we highly recommended converting microscopy image files to ome.tiff before uploading them to OMERO (with in-place import or not).

For that, we highly recommend the tool https://www.glencoesoftware.com/products/ngff-converter/

Download the appropriate installer (.dmg for mac, .msi for windows) and start it.

Drag and drop a file and choose "OME-TIFF" as output file format (OME-NGFF converts to the formats "ome.zarr" and will be discussed in a different page).

Choose set as default to not input it each time.

Additional settings can be changed to increase for example the number of parallel workers (will speed up the conversion). Advanced settings should be used with caution.

Note that there are separate settings for the conversion to ome.ngff (zarr) and to ome.tiff  Both have an impact when converting to ome.tiff, as images are first converted to ome.ngff before being assembled into an ome.tiff

The resulting image may become smaller than the original. Generated are always losslessly compressed, so this is due to the source image using sometime less efficient compression.