[ome-users] file export

[Jason Swedlow]

Hi Martin-

All good points.  These are clearly important.  A few things-

you can already save any image you are viewing in OMERO.insight--  
just click on the diskette icon in the toolbar-- this makes a  
jpeg, .bmp, or .png file.  Obviously, these are not data files-- they  
are more for presentation.

We have waited on supporting OME-TIFF export for a whole bunch of  
technical reasons, mostly having to do with ensuring all our data  
modeling details were up-to-date.  this work is largely done, so we  
can now consider this.

One problem we have with display of multi-channel images is to decide  
what color to display them as.  Currently, we just use a default--  
channel 1 is blue, channel 2 is green, and so on.   Since we have to  
support many file formats, it gets a bit tricky to satisfy everyone--  
making sure your images appear in OMERO exactly as they appeared in  
your normal software is a real challenge.  . however, when we have  
channel metadata, we could use the channel value to guide the color  
of the display.  When we don't have this metadata, what should we  
do?  Any suggestion for an intelligent guess?

Cheers,

Jason


On 5 Aug 2008, at 05:31, 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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