[ome-devel] Opera Flex file lattest changes

[Melissa Linkert]

Hi Anatole,

>   On a related note, it seems that those new flex files are sometime
> loaded incorrectly. I reported it a while back
> (https://trac.openmicroscopy.org.uk/ome/ticket/11382 I think). I can
> confirm the issue is still present in 5.0.

Thank you for the follow-up; as posted on the ticket and in a different
thread, we do now have a proposed fix for this problem:

https://github.com/openmicroscopy/bioformats/pull/1018

Regards,
-Melissa

On Tue, Mar 25, 2014 at 10:45:35AM +0000, Anatole Chessel wrote:
> 
> Hi all
> 
>   On a related note, it seems that those new flex files are sometime
> loaded incorrectly. I reported it a while back
> (https://trac.openmicroscopy.org.uk/ome/ticket/11382 I think). I can
> confirm the issue is still present in 5.0.
> 
> 
> Thanks
> Anatole
> 
> 
> On 19/03/2014 17:39, Balaji Ramalingam wrote:
> >Hi,
> >
> >Here's more,
> >All the API calls are documented in here,
> >Please search for getWells*/getPlate*,
> >
> >http://downloads.openmicroscopy.org/bio-formats/5.0.0/api/ome/xml/meta/MetadataRetrieve.html
> >
> >That should give you all the options that are supported (and the
> >signatures as well).
> >Once we get the files, I can suggest a small code snippet to
> >extract the details as requested.
> >
> >Best,
> >Balaji
> >
> >From: Balaji Ramalingam <b.ramalingam at dundee.ac.uk
> ><mailto:b.ramalingam at dundee.ac.uk>>
> >Date: Wednesday, 19 March 2014 15:24
> >To: "Bonamy, Ghislain" <ghislain.bonamy at novartis.com
> ><mailto:ghislain.bonamy at novartis.com>>,
> >"ome-devel at lists.openmicroscopy.org.uk
> ><mailto:ome-devel at lists.openmicroscopy.org.uk>"
> ><ome-devel at lists.openmicroscopy.org.uk
> ><mailto:ome-devel at lists.openmicroscopy.org.uk>>
> >Subject: Re: [ome-devel] Opera Flex file lattest changes
> >
> >Hi,
> >
> >The following page lists the supported metadata fields for the
> >flex format,
> >http://www.openmicroscopy.org/site/support/bio-formats4/formats/evotecperkinelmer-opera-flex-metadata.html
> >
> >It would be great if you could upload a sample set (images from
> >one or two wells) to ,
> >http://qa.openmicroscopy.org.uk/qa/upload/?
> >
> >This will allow us to check the files locally and suggest suitable
> >API calls.
> >
> >Best,
> >Balaji
> >
> >From: <Bonamy>, Ghislain <ghislain.bonamy at novartis.com
> ><mailto:ghislain.bonamy at novartis.com>>
> >Date: Monday, 17 March 2014 11:27
> >To: "ome-devel at lists.openmicroscopy.org.uk
> ><mailto:ome-devel at lists.openmicroscopy.org.uk>"
> ><ome-devel at lists.openmicroscopy.org.uk
> ><mailto:ome-devel at lists.openmicroscopy.org.uk>>
> >Subject: [ome-devel] Opera Flex file lattest changes
> >
> >Hi everyone,
> >
> >It has been a while since I last posted. I had a quick question,
> >which Melissa can probably answer. The flex file form changed
> >slightly in v2.0 of Evoshell. In particular the file structure.
> >The microscope now generates the files as 1 file per field (as
> >opposed to one file per image). As before the rest of the
> >dimensions (ie. Z-stacks and channels) are encoded into the same
> >file.
> >
> >I was wondering how I could request the metadata for a full well
> >in s ingle call? In particular I would like to make our webservice
> >that retrieves the images compatible with the previous version
> >with as little changes as possible. If there was a way to do
> >things like:
> >
> >1)Get the number of fields for Well B01 (002001*)
> >
> >2)Get the image slice for WellB01 Channel2, Z-stack
> >
> >That would be perfect.
> >
> >Thanks in advance for the help. Hopefully this is clear, otherwise
> >I can post more details.
> >
> >Best,
> >
> >Ghislain Bonamy, PhD
> >
> >__________________________________________
> >
> >Group Leader
> >
> >Novartis
> >
> >Institute for
> >
> >Tropical
> >
> >Diseases
> >
> >
> >The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> >The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> >
> >_______________________________________________
> >ome-devel mailing list
> >ome-devel at lists.openmicroscopy.org.uk
> >http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
> >-- 
> >Anatole Chessel, PhD
> >Research associate
> >University of Cambridge
> >Tennis Court Road, Cambridge CB2 1PD
> >tel: +44 (0)1223 334065

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