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Following on from George...

There is no "natural' way to represent in colour a range of  
fluorophores that extend beyond the visible spectrum: what colour is  
Cy5 or Cy7... and if you have to represent four or more channels of   
fluorophores, it's obvious that you can't do that with a simple RBG  
mapping. (As an aside, this is a fatal flaw in the arguments of those  
folk who would try to sell you a colour camera for you fluorescence  
microscope...)

In general, we do not use pure RBG based colours for publishing: we  
usually shift the blue channel more to cyan, the red a little more to  
yellow and the green where ever there is a bit of colour space left.  
We've found that this makes for a much better transition into CMYK  
space for printing.

Two positive points in all this: we've found that some journals really  
do a superlative job in colour reproduction: most notably the Journal  
of Comparative Neurology. And we have done a version of what George  
suggests, using binary outlines to indicate one of the channels (using  
monochrome overlays: see J Comp Neurol 459: 25-43, 2003.) So N=1 more  
at least!!


As one who learnt microscopy in the days requiring vast afterhours in  
the darkroom, I can assure you that it was still relatively easy to  
alter images unethically, and human nature being what it is, I know of  
several examples when such activity happened...

hope that helps

IAN



On Saturday, June 16, 2007, at 12:03  PM, George McNamara wrote:


Hi Jerry,

Guns don't kill people, Photoshop does not kill ethics.

With respect to color figures: Having had figures from several  
manuscripts almost botched by the pre-press operations, I agree  
completely (including, my article on color balancing histology images,  
http://home.earthlink.net/~geomcnamara/McNamara2005JoH28n2pp81-88.pdf).

With respect to fluorescence images, print the individual channels in  
monochrome (black and white sounds soooo binary). This fetish for  
having fluorescein channel images green and DAPI blue, leads to  
'reduction to absurdity' when it comes to printing fluorescent images  
of tryptophan, Cy7, QD800 and IRDye800. Monochrome also helps the 7+%  
of scientists who are color-blind (sorry, I have no easy solution for  
the blind).

I have been encouraging colleagues for years to convert DAPI or Hoechst  
stained nuclei images into binary outlines, and publish them as either  
blue, cyan or white lines, depending on the content of the other  
channels. The number of colleagues who have taken my advice so far is  
N=0.

The editors of the journals mentioned in this thread are suffering from  
megapixels on the brain when they should be requiring the authors to  
report the number of observations. All to often, N=1.

As for Nature (the journal, not our surroundings), these are the people  
who published Benveniste et al 1988 Nature 333: 816-818 (citation found  
in  
http://www.tilgher.it/(nznzh455kieu0p2z4m4vhxn5)/ 
googleframe.aspx?fle=%2fchrCorrelati%2fupload%2fdoc%2fRB_Benveniste.pdf& 
lnk=%2findex.aspx%3ftpr%3d4%26act%3dfscone%26id%3d since Nature doesn't  
have the guts to index it online). As for JCB, my one experience (in  
1986) with their editorial process and integrity: [expletive deleted].


Sincerely,


George






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Anatomy & Histology
Flinders University
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