[ome-users] Importing large image series and Cell^R data

Colin Rickman c.rickman at hw.ac.uk
Mon May 13 20:48:36 BST 2013


I'm just testing our new OMERO installation and have a few questions/problems with importing.

1. I'm uploading a 740,000 frame tiff series with a total size just over 90GB. Using the importer it says uploading 0 of 1 so I assume it has decided to convert it to a single multidimensional ome.tif. After 15 hours it failed with the statement file invalid. My questions are, is there a maximum upload size, is there a maximum ome.tif size, how can I choose to upload all files of a series as a series rather than convert them in to one file?

While this was uploading I attempted to convert the series to an ome.tif in FIJI and this failed at just over 4GB. FIJI was able to convert the series to a single .tif without any problems.

2. My other problem is uploading Olympus Cell^R/Cell Excellence data. Bioformats in FIJI seems to understand the database structure ok but in OMERO it uploads some of the data and names them after the database file names (e.g. xxxx.apl now contains image data) rather than the data names.



Dr Colin Rickman
Institute of Biological Chemistry, Biophysics and Bioengineering
School of Engineering and Physical Sciences
Heriot-Watt University
EH14 4AS

Tel: +44 131 4514193 (Office)


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