[ome-users] file export

[Curtis Rueden]

Hi Martin,

Right now the easiest way to convert your proprietary microscopy data
into OME-TIFF is to use Bio-Formats -- either the Bio-Formats Exporter
ImageJ plugin, or the bfconvert command line tool. See
http://www.loci.wisc.edu/ome/formats.html for details. I do think the
features you describe would be very appropriate for a future release
of OMERO, though.

-Curtis

On Tue, Aug 5, 2008 at 4:31 AM,  <josh.moore at gmx.de> wrote:
>
> Forwarding to list.
>
>> Hi Josh,
>>
>> thanks very much for the quick reply. Well, right now I simply
>> wanted a quick way of converting confocal images to something
>> useful for various other software, and because the standardised
>> file format is one of the main strengths of OME / OMERO, it was
>> obvious to me to try it. Another major reason is that we are in
>> the process of building up a test run in Imperial College, in
>> collaboration between my microscopy facility, CISBIC (systems
>> biology) and some people in physics. So I have started to use
>> OMERO for real-life images, and was actually very surprised that
>> you can import everything, but can't get it back out. Because
>> OMERO is mainly a database, not an image processing tool, which is
>> only just started to be implemented.
>>
>> I know there are beginning to be interfaces with some bits of
>> software, like CellProfiler or Imaris, but that will never work
>> with all software.
>>
>> So I propose the following export functions for a selection of
>> images (from the image browser):
>>
>>   * a few basic file formats (OME-TIFF, jpg, gif, png)
>>   * assignment of channels into RGB channels (similar to Zeiss LSM export)
>>   * ideal (that's what I would have needed recently): export of a
>>   * few special views like maximum projection or tiled channel
>>     view
>>   * possible long-term optimisation: movie export
>>
>> Please let me know if anything like this is already planned or in
>> progress.
>>
>> Best regards,
>>
>> Martin
>
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