[ome-users] Importing Metamorph stacks is slow with OMERO-5.0.0

[Damien Goutte-Gattat]

Dear All,

After upgrading to OMERO-5.0.0, I have found that importing Metamorph ND
files took a very long time.

For instance, importing a stack made of 3 channels, 12 Z-slices and 32
T-frames took more than 90 minutes. Importing the same kind of stack
used to take no more than a few minutes with OMERO-4.4.9.

In comparison, on the same server importing a Leica LIF file containing
2 channels, 12 Z-slices and 50 T-frames only took a couple of minutes.

As most of my images are acquired using Metamorph, this slow import into
OMERO is very inconvenient, and any help to reduce the import time would
be much appreciated.

I can provide the ND file if needed (570 MB), as well as the log file
generated by OMERO when importing it (72 MB).

Sincerely,

Damien


P.S.: I don’t know if that may help or if it is even relevant, but I
found many occurences of the following lines in the log file:

---8<------
Plane:0 X:0 Y:0 TileWidth:510 TileHeight:8 arrayBuf.length:8160
Plane:0 X:0 Y:8 TileWidth:510 TileHeight:8 arrayBuf.length:8160
Plane:0 X:0 Y:16 TileWidth:510 TileHeight:8 arrayBuf.length:8160
[...]
Plane:0 X:0 Y:496 TileWidth:510 TileHeight:8 arrayBuf.length:8160
Plane:1 X:0 Y:0 TileWidth:510 TileHeight:8 arrayBuf.length:8160
Plane:1 X:0 Y:8 TileWidth:510 TileHeight:8 arrayBuf.length:8160
--->8-------

Whereas in the log file generated when importing the Leica file, I found
something like that:

---8<------
Plane:0 X:0 Y:0 TileWidth:512 TileHeight:512 arrayBuf.length:262144
Plane:1 X:0 Y:0 TileWidth:512 TileHeight:512 arrayBuf.length:262144
Plane:2 X:0 Y:0 TileWidth:512 TileHeight:512 arrayBuf.length:262144
--->8------

I am not sure I really understand what’s going on here, but to me it
looks like that for the Metamorph file, each plane (of size 510×504) is
read in 63 blocks of 510×8 pixels, while for the Leica file, each plane
(of size 512×512) is read in a single block.

Could this explain why importing the Metamorph file is dramatically
slower than importing the Leica file?

-- 
Damien Goutte-Gattat        Institut Européen de Chimie et Biologie
                            2 rue Robert Escarpit
Tel: +33-5-4000-2951        33607 Pessac, FRANCE
E-mail: d.goutte-gattat at iecb.u-bordeaux.fr

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