http://imagej.273.s1.nabble.com/Wavelength-to-RGB-coversion-tp3687192p3687193.html
Thanks for your comments Dr. White. I understand the problems associated
with assigning RGB colors to wavelengths. Several software packages have
wavelength coloring functions (e.g. ImageJ, Zeiss, MetaMorph, Volocity)
colorization scheme to a z-stack automatically. I was able to accomplish
> Hi Esteban,
>
> On Aug 7, 2010, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
> > Date: Fri, 6 Aug 2010 12:21:59 -0700
> > From: "G. Esteban Fernandez" <
[hidden email]>
> > Subject: Wavelength to RGB coversion
> >
> > I have 4D (xyz + lambda/spectral) stacks from a Zeiss 710 confocal that I
> > need to render in 3D, with the lambda dimension pseudocolored in RGB.
> > Zeiss AIM/LSM and ZEN software do not render 3D volumes of lambda-colored
> > z-stacks or even export series of lambda-colored planes to TIFF (I'd have
> to
> > do 'em one by one)
>
> there is a very good reason why it does not do that.....
>
>
> > so I'm going to color each channel according to
> > wavelength using ImageJ's Image5D format. Might there be an ImageJ
> plugin
> > or other software that reads the metadata and does this automatically?
> >
> > Thanks,
> > Esteban
>
> The problem here is that there is no reliable/robust way to convert a
> wavelength into an RGB colour.
>
> 1) what will you do for far red wavelengths that are invisible to the eye?
> Have them be invisible?
> Use some other arbitrary colour... which you then cant use for the
> wavelength that looks most like it?
>
> 2) Similarly in the UV, you have a problem also. It has no human perceived
> colour to map to.
>
> 3) Worse still our eyes are most sensitive to Green, less to to red, and
> worst to Blue.
> This is biology - not much you can do about it.
> It mean that you can not compare the brightness of a green pixel
> with that of a blue one,
> even when they have the same intensity value, the green will
> "look" brighter.
>
> This basically makes a nonsense of the whole idea of trying to "see"
> all the wavelengths at the same time.
> There is simply too much in a spectral, xyz, scan for our eyes and
> brain to deal with in any useful way
> (other than just looking pretty - art not science)
>
> A good read of
>
http://en.wikipedia.org/wiki/Color_vision> and other similar pages might help you get the idea.
>
>
> What you really need to do is some data reduction trick,
> where you throw away info that is not interesting, abut keep the stuff that
> you want to see.
> Its about seeing the wood, despite the trees.
>
> As is often the case,
> your actual problem here is not on trying to do the multi wavelength
> visualisation
> (which, as I explain above, will not give you a final image that you are
> able to easily interpret scientifically)
> but rather that you need to define better what it is that you want to
> actually visualise,
> and reduce the dimensionality of the data and its complexity to such a
> state
> that you can visualize what it is that you are after.
>
> if you want to chat about it off list, feel free to contact me!
>
> cheers
>
> dan
>
>
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
>
http://www.bioimagexd.net BioImageXD
>
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries
> Included)
>
http://www.chalkie.org.uk Dan's Homepages
>
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
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