[ome-users] OMERO 5.0 .nd import question

[Christophe TREFOIS]

Dear all,

Why does it seem when importing a Metamorph .nd stack, that only 2 pixels by 2 pixels are being read in ?
A TileHeight of 2 seems to be extremely inefficient.

If anybody knows what could be going on here that would be great.

Just as an info, but a .nd linking to ~70 MB of images, is taking more than 40 mins to still not finish importing...

Thank you,

2014-02-04 05:10:50,663 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:0 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:50,666 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:50,679 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:51,017 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:51,024 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:2 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:51,027 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:51,041 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:51,377 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:51,382 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:4 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:51,384 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:51,398 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:51,721 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:51,727 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:6 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:51,729 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:51,743 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:52,100 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:52,106 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:8 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:52,109 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:52,125 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:52,530 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:52,624 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:10 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:52,628 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:52,649 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:53,021 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:53,027 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:12 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
2014-02-04 05:10:53,030 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-02-04 05:10:53,044 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-02-04 05:10:53,458 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-02-04 05:10:53,464 DEBUG [    o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:14 TileWidth:1392 TileHeight:2 arrayBuf.length:5568


................................................................................

Dipl.-Ing. Christophe TREFOIS
Ing. Sys. Com. Dipl. EPF

PhD Candidate


Université du Luxembourg | University of Luxembourg

Campus Belval | House of Biomedicine

7, avenue des Hauts-Fourneaux

L-4362 Esch-sur-Alzette

T +352 46 66 44 6124
F +352 46 66 44 6949
www.uni.lu/lcsb<http://www.uni.lu/lcsb>


This message is confidential and may contain privileged information.
It is intended for the named recipient only.
If you receive it in error please notify me and permanently delete the original message and any copies.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140204/5853386c/attachment.html>