[ome-devel] Fwd: RE : [Fwd: SPIM Data Storage Proposal]

[Jason Swedlow]

Forwarding to list, per AM.

Cheers,

Jason

Begin forwarded message:

> From: Amina MAANDHUI <amina.maandhui at itav-recherche.fr>
> Date: 7 January 2011 00:25:00 GMT
> To: "ajpatterson at lifesci.dundee.ac.uk" <ajpatterson at lifesci.dundee.ac.uk 
> >, "jason at lifesci.dundee.ac.uk" <jason at lifesci.dundee.ac.uk>
> Subject: RE : [Fwd: SPIM Data Storage Proposal]
>
> Hello Jason and Andrew,
>
> I shall start with a few things to know about me.
>
> I am MAANDHUI Amina the one who made up a program using the Labview  
> software. It aims to control the SPIM that my team has been  
> developping  in our lab in Toulouse.
> I work with Guillaume GAY and Corinne LORENZO met several times  
> during the SpimWorkshop in Dublin.
> So, please e-mail me any hot news at: amina.maandhui at itav- 
> recherche.fr.
>
> Then, I would like to congratulate you for this proposal.
> Indeed, it was nowhere near easy to work properly as long as we  
> lacked the storage of
> angles and objectives data in the previous shema. So well done!
>
> In fact, the SPIM we developped have the followings devices:
>
> -- Fluorescence excitation
>
>  -several lasers
>  - AOTF
>  - optical fiber
>  - beam expander
>  - aperture
>  - cylinder lense
>           - objective
> - Sample stage:
>
>    - x,y,z and theta   (independent motorized axes)
>
>  - Emission beam path:
>
>  - objective
>  - motorized filter wheel
>  - tube lens
>  - cooled CCD camera
>
> In other words we use two objectives and four axes that we  
> definitely need to store in the xml file.
>
> I am currently trying to write an xml file under the Labview  
> software using the current shema.
> As soon as I finish I will send you it  in order to compare and  
> discuss about other missing parameters.
> It will also be a way to share our work with all SPIM users and  
> developers. This will help us keep up best collaboration.
>
> Best Regards,
>
> MAANDHUI Amina
>
>
>
>
>
>
> ________________________________________
> De : Guillaume Gay [gay at cict.fr]
> Date d'envoi : jeudi 2 décembre 2010 16:13
> À : Amina MAANDHUI
> Objet : [Fwd: SPIM Data Storage Proposal]
>
> Salut,
>
> Je ne sais pas si tu as reçu ça..
>
> Je n'ai pas trop le temps de regarder. Ceci dit, si t'as des  
> questions,
> pas de pb.
>
> À +
>
> Guillaume
>
> -------- Message transféré --------
>> De: Andrew Patterson <ajpatterson at lifesci.dundee.ac.uk>
>> À: ome-devel at lists.openmicroscopy.org.uk,
>> ome-users at lists.openmicroscopy.org.uk
>> Cc: Kees Weijer <c.j.weijer at dundee.ac.uk>, Guenter Giese
>> <Guenter.Giese at mpimf-heidelberg.mpg.de>, Olaf Selchow
>> <selchow at zeiss.de>, Bernhard Weiss <bernhard.weiss at zeiss.de>, Untzizu
>> Elejalde <U.Elejalde at dundee.ac.uk>, tomancak at mpi-cbg.de,
>> stelzer at embl.de, emmanuel.reynaud at ucd.ie, power at zeiss.de,
>> huisken at mpi-cbg.de, ernst.stelzer at physikalischebiologie.de,
>> elagachado at gmail.com
>> Sujet: SPIM Data Storage Proposal
>> Date: Thu, 2 Dec 2010 13:51:49 +0000
>>
>> Hello SPIM users and developers,
>>
>> We have been in talks with various groups from the SPIM community,  
>> Single (or Selective) Plane Illumination Microscopy, about how they  
>> can store data from this new and expanding field in the OME data  
>> formats. We were fortunate enough to be able to look at some of the  
>> data people are already collecting and discuss it with them.
>>
>> What we have now is a proposal of how to store the data in the  
>> current schema. We have a page detailing this proposal and a sample  
>> available at:
>> http://www.ome-xml.org/wiki/SPIM/InitialSupport
>>
>> We hope this puts in place a file format you can store your data in  
>> but we would welcome the answer to some questions:
>> * What have we missed?
>> * Can people work with these structures?
>> * Are they sufficient for your needs?
>>
>> Any comments would be appreciated,
>>
>> Andrew
>>
>> --
>> Andrew Patterson
>> Software Developer, Open Microscopy Environment
>> Wellcome Trust Centre for Gene Regulation and Expression
>> University of Dundee
>
>



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