Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
On behalf of the other developers of the Open Microscopy Environment
(OME) we wanted to take the opportunity to confirm what Karl mentioned.
OME is being actively developed with improved support for metadata
extraction and annotation currently being added. OME currently supports
many file formats (Applied Precision softworx, Bio-Rad .pic, Zeiss LSM,
generic TIFF, MetaMorph STK, DiscoveryOne screening format) with others
on the way. A current priority for the project is to add real metadata entry
tools, leveraging some ontologies from MGED, GO, etc (available later in
year). OME allows the output of data as XML, that includes all the metadata,
providing a self-describing format for data reporting. Code for
Client-side image analysis tools such as VisBio and Imagej is being
developed so that they directly communicate with OME.
A importer for .lei does not yet exist but we do hope at some point to
add this. If someone would be interested in developing this (using the
other importers as a example) the OME group would be happy to help.
For those that have questions about OME I encourage you to join the OME
discussion forum at http://www.openmicroscopy.org/getting-involved/
best regards,
kevin
Kevin W. Eliceiri
Assistant 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: Karl Garsha <[log in to unmask]>
Date: Tuesday, February 15, 2005 3:41 pm
Subject: Re: Confocal Metadata
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Greetings Bill,
> The Open Microscopy Environment (http://www.openmicroscopy.org; also
> http://www.loci.wisc.edu/ome/) is an open source database driven
> software for multidimensional microscopy; there are proprietary
> solutions as well. The OME file format is supported by some
> manufacturers directly, there are readers available for file formats
> used by some platforms as well. VisBio
> (http://www.loci.wisc.edu/visbio/) is a cross-platform multi-
> dimensionaldata analysis program which is freely available, I
> believe it will open
> Zeiss *.lsm, Bio-Rad PIC, Metamorph STK, Fluoview, Openlab LIFF, Zeiss
> ZVI and other data formats and allow saving to the OME database.
> Thereis an adapter for ImageJ available as well.
> The Leica strategy towards multi-dimensional data is a little
> different in that the slices of a dataset are saved as individual
> *.tiffiles, and meta-data is contained in a separate "header" file
> at the top
> of the directory containing the associated data. This makes it tricky
> to write a dataset opener because it has to parse the header file
> containing information for all of the datasets, and then correctly
> associate the image files with the dataset based on the information
> encoded into the name of each individual tiff file. From this point,
> the file reader has to read the image data and incorporate it into
> somesort of nested data structure which can then be converted to other
> formats. I haven't seen many software packages that can parse the
> Leicaheader file (I believe Amira, Volocity and Imaris will). I
> once wrote a
> *.lei reader based on Python/VTK/WxWindows API's but never finished
> theconversion part because I got busy with other things. Imaris
> supportsOME to the best of my knowledge, I can't remember if the
> other packages
> do too. Improvision (makes Volocity) has thier own image database
> solution, as does BitPlane (makes Imaris).
> Regards,
> Karl
>
> Bill Reed wrote:
>
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > As Confocal microscopes allow entry of metadata at the time of file
> > creation, does anyone know of any software tools that can extract
> that> metadata from the file and create attributes for future
> search and
> > retrieval? Or extract specific words from the .lei file name
> metadata> that can be searched on, say for FDA reporting, etc? Just
> curious. --Bill
> >
> > Bill Reed
> > ABREVITY, Inc.
> > 408-771-7491
> > [log in to unmask] <mailto:[log in to unmask]>
> > www.abrevity.com <http://www.abrevity.com>
> >
> >
>
>
> --
> Karl Garsha
> Light Microscopy Specialist
> Imaging Technology Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> 405 North Mathews Avenue
> Urbana, IL 61801
> Office: B650J
> Phone: 217.244.6292
> Fax: 217.244.6219
> Mobile: 217.390.1874
> www.itg.uiuc.edu
>
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