[ome-users] Fwd: file export

Wed Aug 6 12:04:57 BST 2008

Forwarding to list.

Cheers,

Jason

Begin forwarded message:

> From: Martin Spitaler <m.spitaler at imperial.ac.uk>
> Date: 6 August 2008 04:54:14 GMT-04:00
> To: Jason Swedlow <jason at lifesci.dundee.ac.uk>
> Subject: Re: [ome-users] file export
>
> Hi Jason,
>
>  if anything, the communication on OMERO works perfectly well -  
> good job, everyone!!
>
>  Re: export, I perfectly understand that you can't do everything at  
> once, but the feedback routes work, so looking forward to it. But  
> what I wonder: You have been using OMERO routinely already, how did  
> you handle the interaction between OMERO and data analysis? Analyse  
> the original data and upload again? Or with a manual Blitz-style  
> interface?
>
>  Re: channels: for a start, I wouldn't bother to much with  
> automatic colour assignment, I would rather ask the user at import  
> which colour s/he wants for which channel, and use the last user  
> choice as default (remember one LAST SETTING per file type). Maybe  
> an additional DEFAULT button which writes 1->Red // 2->Green // 3->  
> Blue (do you really use BGR instead of RGB? Even microscopy  
> software tends to use channels in an RGB-like way). I'm used to  
> this from the LSM export, and I think it's the most simple and  
> efficient solution.
>   As development advances, you could later then add an additional  
> option (button) to guess colours from the metadata, or even fancy  
> LUTs.
> By the way, on the list of companies that write OME-XML or OME-TIFF  
> you can add Compix (Hamamatsu) SimplePCI. For some reason I'm  
> trying to identify the metadata don't transfer between SimplePCI  
> and Volocity (still need to check Omero), but I don't know yet who  
> of them is wrong.
>
> Looking forward to the next developments,
>
> Martin
>
> Jason Swedlow wrote:
>> 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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>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
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>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> phone (01382) 385819
>> Intl phone:  44 1382 385819
>> FAX   (01382) 388072
>> email: jason at lifesci.dundee.ac.uk
>>
>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
>> Open Microscopy Environment: http://openmicroscopy.org
>> **************************
>>
>> The University of Dundee is a Scottish Registered Charity, No.  
>> SC015096.
>>
>>
>>

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.