[ome-users] Flex File Format

Sun May 3 21:04:03 BST 2009

Hi Jason,

Thanks for the feedback! Let me try to clarify a few points:

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.

GB: What I meant here is that many new tags are supported; however some of the critical one are not correctly handled. I do not believe that that I am using any special files, but rather that the way to extract the number of z-sections, fields etc. has not been implemented. I talked about his with Melissa a few months ago, and perhaps we can take this discussion off-line with users interested in FLEX file reader improvements in bioformats.

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&E 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.

GB: Yes I was referring to PerkinElmer. I am glad to hear that they provided file examples, although I still hope that perhaps they will provide some actual coding/testing support to allow full handling of their FLEX file format. As mentioned above, I do not think that the flex files that I am using differ from the one they have provided. I believe it is more a matter of parsing out the full information contained in their metadata.

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) see 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.

GB: I am not suggesting writing a proprietary file format, although I see why it may sound like it. One of the limitations with using the OME-TIFF model is that the file becomes incompatible with the vendors tools. It seems that the format selected by P&E is very good in the sense that it builds on a format logic closely related to OME-TIFF. Thus, I though enabling creation of chimeric files could be useful for formats in which it can be implemented (manly with Tiff derivative formats). I wrote this in relation to importing files into OMERO, which was the purpose of the original thread. If Flex flex files can be converted as OME.TIFF, but retain the flex file characteristics (ie. flex extension + correct IFID), this would make it very convenient. I suppose that an easier (and perhaps  better) alternative would be to generate an OME-TIFF file were the pixel data points to the flex file? Could this work and allow users to import there flex files into OMERO?

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&E 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.

GB: Agreed, just brought it up for users employing Luraware compression and hoping to get a response from people at P&E, to see if it would be feasible within their licensing agreement with Luraware to provide a license key to their Opera users. In particular for working with OMERO with compressed FLEX files.

Let me know if my points remain unclear.

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/ <http://www.gnf.org/> > 

HudsonAlpha Instiute for Biotechnology
www.hudsonalpha.org <http://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

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

**************************

Wellcome Trust Centre for Gene Regulation & Expression

College of Life Sciences

MSI/WTB/JBC Complex

University of Dundee

Dow Street

Dundee  DD1 5EH

United Kingdom

phone (01382) 385819

Intl phone:  44 1382 385819 

FAX   (01382) 388072 

email: jason at lifesci.dundee.ac.uk <mailto:jason at lifesci.dundee.ac.uk> 

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/ <http://www.dundee.ac.uk/lifesciences/swedlow/> 

Open Microscopy Environment: http://openmicroscopy.org <http://openmicroscopy.org/> 

**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.