Wavelength to RGB coversion
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G. Esteban Fernandez |
Wavelength to RGB coversion
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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) 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
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Craig Brideau |
Re: Wavelength to RGB coversion
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Our ImageTrak software can handle spectral data and display in RGB.
http://www.ucalgary.ca/styslab/imagetrak It is Mac only though. Craig On Fri, Aug 6, 2010 at 1:21 PM, G. Esteban Fernandez <[hidden email]> wrote: > 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) 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 |
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Hi Esteban, We too face the same problem with 710 meta and Zeiss has no solution for it. We have to do this one by one. Even with ImageJ, it cannot be done automatically. Though, I tried with ImageTrak in the Mac, I could not do the RGB pseudo coloring simultaneously. I guess, we need to ask Zeiss to develop a plugin for this problem. Roshma. On Fri, Aug 6, 2010 at 9:59 PM, Craig Brideau <[hidden email]> wrote: Our ImageTrak software can handle spectral data and display in RGB. |
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There is a real problem with this conversion. You can take
the simplistic option and split the spectrum into three and make those B. G and
R but it isn’t actually right – violet will come out as blue.
Photographic films have the same problem. The way to do it ‘correctly’
is to use the spectral response of the three visual pigments but it’s
much harder work and I don’t know of any software which will do
this. Of course it could be done.
Guy Optical Imaging Techniques in Cell Biology by Guy Cox CRC Press / Taylor & Francis http://www.guycox.com/optical.htm ______________________________________________ Associate Professor Guy Cox, MA, DPhil(Oxon) Australian Centre for Microscopy & Microanalysis, Madsen Building F09, University of Sydney, NSW 2006 Phone +61 2 9351 3176 Fax +61 2 9351
7682
Mobile 0413 281 861 ______________________________________________ From: Confocal Microscopy List
[mailto:[hidden email]] On Behalf Of Roshma Azeem
On Fri, Aug 6, 2010 at 9:59 PM, Craig Brideau <[hidden email]> wrote: Our ImageTrak software can handle spectral data and display
in RGB.
No virus
found in this incoming message. |
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Craig Brideau |
Re: Wavelength to RGB coversion
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In reply to this post by Roshma Azeem
The latest version of ImageTrak can do this. Unfortunately it is only
an internal Alpha used amongst our lab group which has not been released on the website. If you contact the author, Dr. Stys, directly he may be willing to let you try the new Alpha version. Craig On Sat, Aug 7, 2010 at 3:17 AM, Roshma Azeem <[hidden email]> wrote: > > Hi Esteban, > > We too face the same problem with 710 meta and Zeiss has no solution for it. > We have to do this one by one. Even with ImageJ, it cannot be done > automatically. Though, I tried with ImageTrak in the Mac, I could not do the > RGB pseudo coloring simultaneously. I guess, we need to ask Zeiss to develop > a plugin for this problem. > > Roshma. > > > > On Fri, Aug 6, 2010 at 9:59 PM, Craig Brideau <[hidden email]> > wrote: >> >> Our ImageTrak software can handle spectral data and display in RGB. >> >> http://www.ucalgary.ca/styslab/imagetrak >> >> It is Mac only though. >> >> Craig >> >> >> On Fri, Aug 6, 2010 at 1:21 PM, G. Esteban Fernandez >> <[hidden email]> wrote: >> > 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) 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 > > |
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