[ome-users] Flex File Format

Sun May 3 19:40:22 BST 2009

Hi Ghislain-

On 2 May 2009, at 16:19, Ghislain Bonamy wrote:

> 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.

Thanks for this feedback.  This is news to us, as we correctly report  
this metadata from the test files we have.  If you have had problems  
using Bio-Formats, the best thing to do is to send us details, and if  
possible, the offending files, and we'll certainly work to we fix any  
problems we find.
>
> 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.

On the contrary, PerkinElmer (I assume that is who you are referring  
to) have been very helpful supplying test files.  Again, if you have  
files that might expose something we don't know about, sending us  
specific details and the data is the best thing to do.

> 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.
>

Can you explain why we should do this?  Why doesn't the metadata in  
OME-TIFF satisfy your needs?  Note that we NEVER directly write  
proprietary formats-- we have enough problems supporting reads of all  
the variants. Writing as well would be a minefield, and more  
importantly, breaks the whole concept of supporting interoperability.
>
>
> 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.

We can't comment on PerkinElmer's plans for file formats; we have no  
knowledge of their plans and agreements and any discussions of this  
with the community and users is up to them.  We do however agree that  
saving data in uncompressed form often leaves the user with many more  
options for data handling and analysis.

Hope that helps.  Thanks again for your feedback.

Cheers,

Jason

>
>
>
>
> Let me know if you have any other questions.
>
>
>
> Best,
>
>
>
> Ghislain Bonamy, PhD
> _______________________________
> Genomic Institute of the
> Novartis Research
> Foundation
> Functional Genomics, G214
> +1 (858) 812-1534 (W & F)
> +1 (858) 354-7388 (C)
> www.gnf.org <http://www.gnf.org/>
>
> HudsonAlpha Instiute for Biotechnology
> www.hudsonalpha.org
> <http://www.gnf.org/>
>
> ________________________________
>
> 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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