[ome-users] Bioformats works only outside OME (more data)

[Mario Valle]

Continuing investigation I have found:

- From the OME web interface I can import only TIFF files. No error, nothing, only
"unrecognized format"

- From the command line: ome import -d "dataset" image
  I can import TIFF, STK, ie. everything except formats supported by the bioformats
  library.

So seems there are two problems:
  1) the bioformats library not found
  2) the web server accessing only a minimal subset of the import functionality.

Help!
	mario


Mario Valle wrote:
> I'm still stuck at the image importing step...
> 
> 1) Moved to OME 2.6.1 on Mac (here I'm administrator, so I can experiment)
> 2) installed latest loci_tools.jar under /OME/java
> 3) downloaded bftools, unpacked and added the same loci_tools.jar ar OME in the resulting
> directory
> 3) tried bfview with TIFF, LIF, LSM, STK, LIFF files. Everything works. Only TIFF with
> character encoding Mac cannot be visualized, but this is another problem.
> 3) tried to import the same files in OME, only the tiff files are imported.
> Seems like OME is using some old import method, but no other copy of loci_tools.jar is
> anywhere on the machine.
> Help!
> 	mario
> 
> 

-- 
Ing. Mario Valle
Visualization Group                              | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82