[ome-devel] OME-HDF

[Daniel.Martens at Olympus-SIS.com]

Dear Kevin,

Thank you for your reply. The core functionality of our software (
http://www.olympus.co.uk/microscopy/22_scan_R.htm)  is to detect, analyse 
and classify particles and generate statistics about found populations. 
The classification is done through a cytometry like interface with several 
histograms, displaying the particles in arbitrary feature spaces. 
Currently we are working on extending the particle capacity to 50m+ 
particles, resulting in about 25gb of uncompressed particle feature data. 
The current data storrage formate is a proprietary, binary one. To 
facilitate exchangeablity and data access we would like to move to a 
standart formate that suports a structure like this:
Project/Experiment      /Sample/Particledata
                        /Settings
                        /Result

Although I did not yet familiarise myself in depth with the OME XML data 
model, it seems to me it could support such a structure. If so we would be 
very interested in a hdf implementation of the ome xml data model.

best regards,

Daniel


Product Unit Life Science Cell Screening

OLYMPUS SOFT IMAGING SOLUTIONS GMBH
Sauerbruchstr. 50, 81377 München, Germany/Deutschland
Phone: +49 (89) 579589 - 6632
E-mail: Daniel.Martens at olympus-sis.com
www.olympus-sis.com

Headquarters Olympus Soft Imaging Solutions GmbH
Johann-Krane-Weg 39, 48149 Münster, Germany/Deutschland
 
Registergericht/Register Court: Handelsregister/Commercial Registry 
Münster, HRB 10405
Geschäftsführer/Managing Directors: Michael Czempiel (Vors.), Dr. Helmut 
Köhler, Masaaki Yamagishi, Koji Fujio

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Kevin W Eliceiri <eliceiri at facstaff.wisc.edu> 
Sent by: ome-devel-bounces at lists.openmicroscopy.org.uk
07/02/2009 21:10
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Subject
Re: [ome-devel] OME-HDF






Dear Daniel,

We in the OME consortium are very interested in developing a "OME-HDF" 
format that would complement the current OME-TIFF and use the OME XML data 
model (http://www.ome-xml.org/). We have actively applied for resources to 
create such a format and have been talking to several interested parties 
about a potential specification and their respective needs for a "OME-HDF" 
format. We would be very interested in hearing more about your application 
and specification needs. 

best regards,
kevin

Kevin W. Eliceiri
Director
Laboratory for Optical and Computational Instrumentation
http://www.loci.wisc.edu
Room 271 Animal Sciences
1675 Observatory Drive
Madison, WI 53706
Phone: 608-263-6288
Fax: 608-262-4570

----- Original Message -----
From: Daniel.Martens at Olympus-SIS.com
Date: Thursday, February 5, 2009 2:49 am
Subject: [ome-devel] OME-HDF
To: ome-devel at lists.openmicroscopy.org.uk


> Dear OME-experts,
> 
> Our group develops a cell screening analysis software, and we are 
> currently looking for a standard format to store the analysis result 
> data. 
> I noticed that the OME-group works on an OME-HDF standard. How far has 
> 
> this format evolved? Is there already a specification of the HDF 
> directory 
> structure?
> 
> Thank you in advance,
> 
> Daniel Martens
> 
> 
> Product Unit Life Science Cell Screening
> 
> OLYMPUS SOFT IMAGING SOLUTIONS GMBH
> Sauerbruchstr. 50, 81377 München, Germany/Deutschland
> Phone: +49 (89) 579589 - 6632
> E-mail: Daniel.Martens at olympus-sis.com
> www.olympus-sis.com
> 
> Headquarters Olympus Soft Imaging Solutions GmbH
> Johann-Krane-Weg 39, 48149 Münster, Germany/Deutschland
> 
> Registergericht/Register Court: Handelsregister/Commercial Registry 
> Münster, HRB 10405
> Geschäftsführer/Managing Directors: Michael Czempiel (Vors.), Dr. 
> Helmut 
> Köhler, Masaaki Yamagishi, Koji Fujio
> 
> Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte 
> Informationen. Wenn Sie nicht der richtige Adressat sind oder dieses 
> E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den 
> Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie 
> die 
> unbefugte Weitergabe dieser Mail ist nicht gestattet.
> 
> This e-mail may contain confidential and/or privileged information. If 
> you 
> are not the intended recipient (or have received this e-mail in error) 
> 
> please notify the sender immediately and destroy this e-mail. Any 
> unauthorized copying, disclosure or distribution of the material in 
> this 
> e-mail is strictly forbidden.
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