[ome-users] Flex File Format

[Ghislain Bonamy]

John,

 

Unfortunately the flex file format is not up to date in the bioformats, although some of the new metadata is handled. In particular, bioformats is unable to retrieve the number of fields/z-section/channels/time point, which is critical point. 

 

I was hoping to work on this and add this capacity to the format but have not had a chance to it. I have contacted P&K about maybe helping out since they are using Omro a base for their Columbus platform, but I don't think, oddly enough, that they are interested to help. Perhaps if enough customer request that they help improving bioformats they might do it. I will try to work on it soon and will keep the Opera users posted. Furthermore, a nice feature would be to be able to keep the metadata from the flex file in addition to the metadata from OME, so that the flex file remains backward compatible with the Epochal (becomes both an ome.tiff and remains a flex file). This feature which could be extended to all TIFF derivative format, may require some serious modifications of bioformats, but I will let the expert (i.e.. Jason) se what they can do about t.

 

On another note bioformats does support the luraware compression, granted hat you provide a license code for it. Logic would suggest that a key would be required to compress with luraware but not to decompress to make the forma at least partially open. This however is not the case. Perhaps P&K should in my opinion provide such license code since the capacity of a user to read an image is obviously a inherent part of their system. However, this may not be part of the agreement they reach with Luraware. In the mean time, saving as uncompressed tiff is the better solution.

 

Let me know if you have any other questions.

 

Best,

 

 Ghislain Bonamy, PhD 
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Genomic Institute of the
Novartis Research
Foundation
Functional Genomics, G214
+1 (858) 812-1534 (W & F)
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www.gnf.org <http://www.gnf.org/> 
 
HudsonAlpha Instiute for Biotechnology
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________________________________

From: ome-users-bounces at lists.openmicroscopy.org.uk on behalf of John Moffat
Sent: Fri 5/1/2009 11:40 PM
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Flex File Format



Hi,
I was just about to ask the exact same question as the previous 
poster. Since I'm not using the Lurawave compression (not worth the 
hassle, in my opinion), is there a way we can activate the 
PerkinElmer .flex format in the bioformats library?

Does anyone know if the flex file bioformat is up to date with the 
newer (Acapella 2) version of the format? Either way, I'd like to test 
it.

Thanks
John


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