[ome-users] Lif file - pre-set colours issue

[Will Moore]

HI Kim,

 Yes it should be fixed by our next release which should be early next year, if not before.

 Cheers,
 
  Will.


On 28 Nov 2011, at 00:02, Kim Linton wrote:

> Hi Will,
> 
> I had a look at the Trac issue - it shows that it is going to be worked on in the 13/12/2011 sprint. Does this mean it will be fixed early next year?
> 
> Cheers,
> 
> Kim
> 
> 
> On 25 November 2011 20:47, Will Moore <will at lifesci.dundee.ac.uk> wrote:
> Hi Kim,
> 
>  Currently, our strategy for setting colours is based on wavelength metadata for each channel.
> This kinda works in many cases, but there are always edge cases where it fails. 
> I forget the cut-offs at the moment, but it's possible that any excitation wavelength of 500 or below is blue. 
> We have attempted to update the cut-offs etc several times, and always find that some file renders incorrectly.
> Yours are 484 and 500nm.
> 
> We are attempting to address this problem for file formats that explicitly specify colours in their metadata:
> http://trac.openmicroscopy.org.uk/ome/ticket/3651
> This includes LIF, LEI & LSM files. 
> 
> You might be interested in a script, submitted to us by Pierre Pouchin, that does this same job after import, based on the Original Metadata:
> http://www.openmicroscopy.org/community/viewtopic.php?f=16&t=920
> 
>  Cheers,
> 
>    Will.
> 
> 
> On 25 Nov 2011, at 00:46, Kim Linton wrote:
> 
>> Hi There,
>> 
>> I've provided a link to a lif file that has the 2 channels. One should be a grey and the other should be green. When I loaded it into OMERO it is not bringing the pre-set colours across - it defaults to blue. Is this normal functionality or an issue?
>> 
>> The file can be located on Cloudstor - https://cloudstor.aarnet.edu.au/filesender/?vid=9B547F3D-666B-0B81-1B09-D82F8FF24253.
>> 
>> Cheers,
>> 
>> Kim
>> 
>> -- 
>> Kim Linton
>> Senior Research Systems Facilitator
>> Monash e-Research Centre
>> Building 75
>> Monash University
>> Clayton Victoria 3800, Australia
>> Ph:      +61 3 99020712
>> Fax:    +61 3 9902-0193
>> Email:  kim.linton at monash.edu
>> Web:    http://www.monash.edu.au/eresearch
>> Part time: Mon, Tues, Thurs & Fri
>> 
>> 
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> 
> 
> 
> 
> -- 
> Kim Linton
> Senior Research Systems Facilitator
> Monash e-Research Centre
> Building 75
> Monash University
> Clayton Victoria 3800, Australia
> Ph:      +61 3 99020712
> Fax:    +61 3 9902-0193
> Email:  kim.linton at monash.edu
> Web:    http://www.monash.edu.au/eresearch
> Part time: Mon, Tues, Thurs & Fri
> 
> 

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