Merging of Images
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Hi,
I am faced with the following problem: A microscopic sample is labelled with 2 fluorescent dyes, one emitting red the other yellow. 2 Images are taken by a black/white camera, one for the red label one, one for the yellow label. Every Image is colourized by a applying the corresponding LUT. My question is know: What would be the best procedure to merge both images? The final image should show both labels in their correct colours. Thanks Christian |
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On Monday 31 Jan 2011 11:55:00 Phase GmbH wrote:
> I am faced with the following problem: > A microscopic sample is labelled with 2 fluorescent dyes, one emitting red > the other yellow. 2 Images are taken by a black/white camera, one for the > red label one, one for the yellow label. Every Image is colourized by a > applying the corresponding LUT. > > My question is know: What would be the best procedure to merge both images? > The final image should show both labels in their correct colours. You can mix yellow and red but this will be a confusing orange, as the hues are not that far away to produce a new distinct additive colou mix. I would rather put the "red" greyscale image (i.e. without LUT) in the blue channel and the yellow signal (which you caputured in greyscale as well) in both the red and green channels. This way ther "red" appears as "blue" and the "yellow" still as "yellow". Cololocalisation appears as white. This can be seen correctly by the vast majority of viewers, including all red-green colour blinds (e.g. protanopes, deuteranopes, and anomalous prot- and deu- dichromats). Another advantage is that they will perceive the colours with the correct names (unlike with the green-magenta pairs that some use). Tritanopes however (a very small proportion of dichromatic viewers) might struggle to see the differences. There is no solution that fits all and preserves colour name perception. Note that the "correct colours" is somewhat misleading as there is no guarantee that the RGB LUT matches the emission spectrum of the dyes. I gave a talk on this subject at the last Luxembourg meeting. Regards Gabriel |
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Hello,
On a related subject, while it's true that it may be impossible to produce color figures that will be understandable by all types of color blind people, it seems that the red/green/blue combination is one of the least desirable. Yet, the red/green/blue colors are the only colors proposed in the Image/Color/Merge Channels tool. Perhaps it might be worth considering allowing the use of more generally discernable colors, like the widely used magenta/green combination or blue/yellow combination noted below. It would be nice, I think, to have these other colors easily accessible in the Merge Channels tool. What do the other users think? Regards, Elizabeth Crowell Gabriel Landini a écrit : > On Monday 31 Jan 2011 11:55:00 Phase GmbH wrote: > >> I am faced with the following problem: >> A microscopic sample is labelled with 2 fluorescent dyes, one emitting red >> the other yellow. 2 Images are taken by a black/white camera, one for the >> red label one, one for the yellow label. Every Image is colourized by a >> applying the corresponding LUT. >> >> My question is know: What would be the best procedure to merge both images? >> The final image should show both labels in their correct colours. >> > > You can mix yellow and red but this will be a confusing orange, as the hues > are not that far away to produce a new distinct additive colou mix. > > I would rather put the "red" greyscale image (i.e. without LUT) in the blue > channel and the yellow signal (which you caputured in greyscale as well) in > both the red and green channels. > This way ther "red" appears as "blue" and the "yellow" still as "yellow". > Cololocalisation appears as white. This can be seen correctly by the vast > majority of viewers, including all red-green colour blinds (e.g. protanopes, > deuteranopes, and anomalous prot- and deu- dichromats). Another advantage is > that they will perceive the colours with the correct names (unlike with the > green-magenta pairs that some use). Tritanopes however (a very small > proportion of dichromatic viewers) might struggle to see the differences. > There is no solution that fits all and preserves colour name perception. > > Note that the "correct colours" is somewhat misleading as there is no > guarantee that the RGB LUT matches the emission spectrum of the dyes. > I gave a talk on this subject at the last Luxembourg meeting. > > Regards > > Gabriel > -- Elizabeth CROWELL ---------------------------------------------------------------------- Membrane Traffic and Cell Division Research Group Institut Pasteur 28 rue du Dr Roux 75015 PARIS, France Tel : 01.44.38.94.07 Fax : 01.45.68.89.54 ---------------------------------------------------------------------- |
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Dear Elizabeth,
if you combine the two channels into a composite image then you have this option in the result. For each channel, you can choose its color with the Channels tool, trigger each channels contrast settings individually and, in case you really want that still, convert that into an RGB image. Using the merge tool, you can achieve the magenta/green combination directly choosing red:image1, green:image2, blue:image1. For combining arbitrary color schemes, you could apply the desired channel-LUT to each of your individual channels, convert each of them to RGB and then use Process->Image Calculator to ADD them. This is essentially what the color merge tool is doing. Best, Stephan On Mon, 2011-01-31 at 14:19 +0100, Crowell Elizabeth wrote: > Hello, > On a related subject, while it's true that it may be impossible to > produce color figures that will be understandable by all types of color > blind people, it seems that the red/green/blue combination is one of the > least desirable. > > Yet, the red/green/blue colors are the only colors proposed in the > Image/Color/Merge Channels tool. > Perhaps it might be worth considering allowing the use of more generally > discernable colors, like the widely used magenta/green combination or > blue/yellow combination noted below. It would be nice, I think, to have > these other colors easily accessible in the Merge Channels tool. > > What do the other users think? > Regards, > Elizabeth Crowell > > > Gabriel Landini a écrit : > > On Monday 31 Jan 2011 11:55:00 Phase GmbH wrote: > > > >> I am faced with the following problem: > >> A microscopic sample is labelled with 2 fluorescent dyes, one emitting red > >> the other yellow. 2 Images are taken by a black/white camera, one for the > >> red label one, one for the yellow label. Every Image is colourized by a > >> applying the corresponding LUT. > >> > >> My question is know: What would be the best procedure to merge both images? > >> The final image should show both labels in their correct colours. > >> > > > > You can mix yellow and red but this will be a confusing orange, as the hues > > are not that far away to produce a new distinct additive colou mix. > > > > I would rather put the "red" greyscale image (i.e. without LUT) in the blue > > channel and the yellow signal (which you caputured in greyscale as well) in > > both the red and green channels. > > This way ther "red" appears as "blue" and the "yellow" still as "yellow". > > Cololocalisation appears as white. This can be seen correctly by the vast > > majority of viewers, including all red-green colour blinds (e.g. protanopes, > > deuteranopes, and anomalous prot- and deu- dichromats). Another advantage is > > that they will perceive the colours with the correct names (unlike with the > > green-magenta pairs that some use). Tritanopes however (a very small > > proportion of dichromatic viewers) might struggle to see the differences. > > There is no solution that fits all and preserves colour name perception. > > > > Note that the "correct colours" is somewhat misleading as there is no > > guarantee that the RGB LUT matches the emission spectrum of the dyes. > > I gave a talk on this subject at the last Luxembourg meeting. > > > > Regards > > > > Gabriel > > > > |
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In reply to this post by Crowell Elizabeth
That would be a very valuable tool for me, so I'm in favor of it!
Regards, Katrien -----Oorspronkelijk bericht----- Van: ImageJ Interest Group [mailto:[hidden email]] Namens Crowell Elizabeth Verzonden: maandag 31 januari 2011 14:20 Aan: [hidden email] Onderwerp: Re: Merging of Images Hello, On a related subject, while it's true that it may be impossible to produce color figures that will be understandable by all types of color blind people, it seems that the red/green/blue combination is one of the least desirable. Yet, the red/green/blue colors are the only colors proposed in the Image/Color/Merge Channels tool. Perhaps it might be worth considering allowing the use of more generally discernable colors, like the widely used magenta/green combination or blue/yellow combination noted below. It would be nice, I think, to have these other colors easily accessible in the Merge Channels tool. What do the other users think? Regards, Elizabeth Crowell Gabriel Landini a écrit : > On Monday 31 Jan 2011 11:55:00 Phase GmbH wrote: > >> I am faced with the following problem: >> A microscopic sample is labelled with 2 fluorescent dyes, one emitting red >> the other yellow. 2 Images are taken by a black/white camera, one for the >> red label one, one for the yellow label. Every Image is colourized by a >> applying the corresponding LUT. >> >> My question is know: What would be the best procedure to merge both images? >> The final image should show both labels in their correct colours. >> > > You can mix yellow and red but this will be a confusing orange, as the hues > are not that far away to produce a new distinct additive colou mix. > > I would rather put the "red" greyscale image (i.e. without LUT) in the blue > channel and the yellow signal (which you caputured in greyscale as well) in > both the red and green channels. > This way ther "red" appears as "blue" and the "yellow" still as "yellow". > Cololocalisation appears as white. This can be seen correctly by the vast > majority of viewers, including all red-green colour blinds (e.g. protanopes, > deuteranopes, and anomalous prot- and deu- dichromats). Another advantage is > that they will perceive the colours with the correct names (unlike with the > green-magenta pairs that some use). Tritanopes however (a very small > proportion of dichromatic viewers) might struggle to see the differences. > There is no solution that fits all and preserves colour name perception. > > Note that the "correct colours" is somewhat misleading as there is no > guarantee that the RGB LUT matches the emission spectrum of the dyes. > I gave a talk on this subject at the last Luxembourg meeting. > > Regards > > Gabriel > -- Elizabeth CROWELL ---------------------------------------------------------------------- Membrane Traffic and Cell Division Research Group Institut Pasteur 28 rue du Dr Roux 75015 PARIS, France Tel : 01.44.38.94.07 Fax : 01.45.68.89.54 ---------------------------------------------------------------------- |
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Dear
The ImageJ version of MacBioPhotonics offers a color merge function (as plugin) which allows to maintain the original LUT of images. Vriendelijke groet, Winnok ___________________________ Winnok H. De Vos, PhD Ghent University - Dept. Molecular Biotechnology Bio-imaging and Cytometry Unit Coupure Links 653 - 9000 Ghent, Belgium Tel: +32 (0)9 264.59.71 - Fax: +32 (0)9 264.62.19 [hidden email] Bioimaging Facility - Light Microscopy Division (LiMiD) Coupure Links 653 - 9000 Ghent, Belgium Tel: +32 (0)9 264.60.84 - Fax: +32 (0)9 264.62.19 [hidden email] On 31 Jan 2011, at 14:36, Katrien Remaut wrote: That would be a very valuable tool for me, so I'm in favor of it! Regards, Katrien -----Oorspronkelijk bericht----- Van: ImageJ Interest Group [mailto:[hidden email]] Namens Crowell Elizabeth Verzonden: maandag 31 januari 2011 14:20 Aan: [hidden email] Onderwerp: Re: Merging of Images Hello, On a related subject, while it's true that it may be impossible to produce color figures that will be understandable by all types of color blind people, it seems that the red/green/blue combination is one of the least desirable. Yet, the red/green/blue colors are the only colors proposed in the Image/Color/Merge Channels tool. Perhaps it might be worth considering allowing the use of more generally discernable colors, like the widely used magenta/green combination or blue/yellow combination noted below. It would be nice, I think, to have these other colors easily accessible in the Merge Channels tool. What do the other users think? Regards, Elizabeth Crowell Gabriel Landini a écrit : > On Monday 31 Jan 2011 11:55:00 Phase GmbH wrote: > >> I am faced with the following problem: >> A microscopic sample is labelled with 2 fluorescent dyes, one emitting red >> the other yellow. 2 Images are taken by a black/white camera, one for the >> red label one, one for the yellow label. Every Image is colourized by a >> applying the corresponding LUT. >> >> My question is know: What would be the best procedure to merge both images? >> The final image should show both labels in their correct colours. >> > > You can mix yellow and red but this will be a confusing orange, as the hues > are not that far away to produce a new distinct additive colou mix. > > I would rather put the "red" greyscale image (i.e. without LUT) in the blue > channel and the yellow signal (which you caputured in greyscale as well) in > both the red and green channels. > This way ther "red" appears as "blue" and the "yellow" still as "yellow". > Cololocalisation appears as white. This can be seen correctly by the vast > majority of viewers, including all red-green colour blinds (e.g. protanopes, > deuteranopes, and anomalous prot- and deu- dichromats). Another advantage is > that they will perceive the colours with the correct names (unlike with the > green-magenta pairs that some use). Tritanopes however (a very small > proportion of dichromatic viewers) might struggle to see the differences. > There is no solution that fits all and preserves colour name perception. > > Note that the "correct colours" is somewhat misleading as there is no > guarantee that the RGB LUT matches the emission spectrum of the dyes. > I gave a talk on this subject at the last Luxembourg meeting. > > Regards > > Gabriel > -- Elizabeth CROWELL ---------------------------------------------------------------------- Membrane Traffic and Cell Division Research Group Institut Pasteur 28 rue du Dr Roux 75015 PARIS, France Tel : 01.44.38.94.07 Fax : 01.45.68.89.54 ---------------------------------------------------------------------- |
Re: Merging of Images
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On Jan 31, 2011, at 8:53 AM, Winnok H. De Vos wrote:
> Dear > > The ImageJ version of MacBioPhotonics offers a color merge function (as plugin) which allows to maintain the original LUT of images. The Image>Color>Merge Channels command in ImageJ 1.44n or later maintains the original LUTs when "Create Composite" is checked in the dialog box. -wayne > On 31 Jan 2011, at 14:36, Katrien Remaut wrote: > > That would be a very valuable tool for me, so I'm in favor of it! > > Regards, > > Katrien > > -----Oorspronkelijk bericht----- > Van: ImageJ Interest Group [mailto:[hidden email]] Namens Crowell > Elizabeth > Verzonden: maandag 31 januari 2011 14:20 > Aan: [hidden email] > Onderwerp: Re: Merging of Images > > Hello, > On a related subject, while it's true that it may be impossible to > produce color figures that will be understandable by all types of color > blind people, it seems that the red/green/blue combination is one of the > least desirable. > > Yet, the red/green/blue colors are the only colors proposed in the > Image/Color/Merge Channels tool. > Perhaps it might be worth considering allowing the use of more generally > discernable colors, like the widely used magenta/green combination or > blue/yellow combination noted below. It would be nice, I think, to have > these other colors easily accessible in the Merge Channels tool. > > What do the other users think? > Regards, > Elizabeth Crowell > > > Gabriel Landini a écrit : >> On Monday 31 Jan 2011 11:55:00 Phase GmbH wrote: >> >>> I am faced with the following problem: >>> A microscopic sample is labelled with 2 fluorescent dyes, one emitting > red >>> the other yellow. 2 Images are taken by a black/white camera, one for the >>> red label one, one for the yellow label. Every Image is colourized by a >>> applying the corresponding LUT. >>> >>> My question is know: What would be the best procedure to merge both > images? >>> The final image should show both labels in their correct colours. >>> >> >> You can mix yellow and red but this will be a confusing orange, as the > hues >> are not that far away to produce a new distinct additive colou mix. >> >> I would rather put the "red" greyscale image (i.e. without LUT) in the > blue >> channel and the yellow signal (which you caputured in greyscale as well) > in >> both the red and green channels. >> This way ther "red" appears as "blue" and the "yellow" still as "yellow". >> Cololocalisation appears as white. This can be seen correctly by the vast >> majority of viewers, including all red-green colour blinds (e.g. > protanopes, >> deuteranopes, and anomalous prot- and deu- dichromats). Another advantage > is >> that they will perceive the colours with the correct names (unlike with > the >> green-magenta pairs that some use). Tritanopes however (a very small >> proportion of dichromatic viewers) might struggle to see the differences. >> There is no solution that fits all and preserves colour name perception. >> >> Note that the "correct colours" is somewhat misleading as there is no >> guarantee that the RGB LUT matches the emission spectrum of the dyes. >> I gave a talk on this subject at the last Luxembourg meeting. >> >> Regards >> >> Gabriel >> > > > -- > > Elizabeth CROWELL > > ---------------------------------------------------------------------- > Membrane Traffic and Cell Division Research Group > Institut Pasteur > 28 rue du Dr Roux > 75015 PARIS, France > > Tel : 01.44.38.94.07 > Fax : 01.45.68.89.54 > ---------------------------------------------------------------------- |
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