[ome-users] 1. Slow upload of large sets of files 2. VTK files?

Sluka, James Patrick jsluka at indiana.edu
Mon Jan 28 21:26:55 GMT 2013

New user here exploring the use of OMERO to log the output from 
multicell modeling projects. Multicell computational models generate 
data sets that are basically images (2D, 3D and 4D). It would be very 
useful to have an archiving system, such as OMERO, that can capture the 
large number of files a simulation generates and that can also capture 
metadata associated with the simulations, for example the complete 
script that generated the simulation.

We have installed OMERO server on a university server. I am testing 
loading simulation output files into the repository from Windows and 
Ubuntu PCs. Two issues have come up:

1. Uploading a large set of PNG files (~30K files total, 5KB/file) 
takes a long time, roughly two minutes per file on an Ubuntu system. 
Uploading a much smaller list of the same types of files is much 
faster, a couple seconds per file. It appears the very large number of 
files is making the time per file very large. Any thoughts on what 
might cause this?

2. Any thoughts on how VTK files might be loaded into OMERO? In 
particular, VTK STRUCTURED_POINTS format files, but any VTK file format 
would be helpful. We use VTK files to store not only the assignment 
data that puts a given pixel (or voxel) into a particular cell of 
particular cell type but to also log pixel values for diffusible fields 
such as oxygen.

Does anyone have any experience using OMERO for this type of 
application (logging of simulation images)?

Thanks for any guidance folks can provide.

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