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

[Ilya Goldberg]

It seems more and more people are struggling with OME server's over- 
riding the new and better bioformats with its old and deprecated  
importers.
See Curits's earlier post about re-arranging the importer priority to  
either eliminate OME's importers altogether, or move bioformats up in  
the priority list.
We will make these changes permanent in future releases so that BF  
takes priority over everything else.

There may be other problems with the connection, but in the default  
configuration, OME's importers will over-ride TIFF, LSM, and STK.   
They should still import them, but apparently there are potentially  
other issues with these files, and BF does a better job.  LIFF and  
LIF should have been delegated to BF, because there are no "native"  
importers for these.  Which makes me think there may be an unrelated  
problem with the BF setup.

-Ilya

On Jan 11, 2008, at 6:31 AM, Mario Valle wrote:

> 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
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