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

[Will Moore]

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
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> 
> 
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