HELP needed from IMAGEJ to Photoshop
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HELP needed from IMAGEJ to Photoshop
 
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Hi, I am in dire need of help with converting imagej files that are saved
as TIFF files to viewing them in Photoshop. In IMAGEJ, my images have 3 separate channels (blue, red, green). My problem is that when I view the split images in photoshop they are gre,. Instead of my split images being blue, red, or green like when I saved them as TIFF files from IMAGEJ they are now grey. Furthermore, when I open those same files "turned" grey back in image they are now grey instead of being their original color (blue red or green). Can someone please help? Thank you -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: HELP needed from IMAGEJ to Photoshop
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Hi balloo02,
While I am not a Photoshop user, I am pretty sure that what you are seeing is correct. I will try to give you an answer in simple words. When you split an image into its colour channels, they essentially become single channel (greyscale) images. So when opening them in Photoshop, there is no way that that application knows that the image opened used to be a colour component of colour image. Are the images identical to each other, or they are slightly different? Of course that heavily depends on what was your original image. Try to merge the colour channel images back to a colour image and check if that will give you your original image. Hope that helps... cheers! On Wed 28 Aug 2013 04:36:05 AM CEST, balloo02 . wrote: > Hi, I am in dire need of help with converting imagej files that are saved > as TIFF files to viewing them in Photoshop. In IMAGEJ, my images have 3 > separate channels (blue, red, green). My problem is that when I view the > split images in photoshop they are gre,. Instead of my split images being > blue, red, or green like when I saved them as TIFF files from IMAGEJ they > are now grey. Furthermore, when I open those same files "turned" grey back > in image they are now grey instead of being their original color (blue red > or green). Can someone please help? Thank you > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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if you can save as jpg in ImageJ then photoshop will open in color,Samuel,
Bangalore, India On Wed, Aug 28, 2013 at 12:53 PM, Dionysios Lefkaditis <[hidden email] > wrote: > Hi balloo02, > > While I am not a Photoshop user, I am pretty sure that what you are seeing > is correct. I will try to give you an answer in simple words. When you > split an image into its colour channels, they essentially become single > channel (greyscale) images. So when opening them in Photoshop, there is no > way that that application knows that the image opened used to be a colour > component of colour image. Are the images identical to each other, or they > are slightly different? Of course that heavily depends on what was your > original image. Try to merge the colour channel images back to a colour > image and check if that will give you your original image. Hope that > helps... > > cheers! > > > On Wed 28 Aug 2013 04:36:05 AM CEST, balloo02 . wrote: > >> Hi, I am in dire need of help with converting imagej files that are saved >> as TIFF files to viewing them in Photoshop. In IMAGEJ, my images have 3 >> separate channels (blue, red, green). My problem is that when I view the >> split images in photoshop they are gre,. Instead of my split images >> being >> blue, red, or green like when I saved them as TIFF files from IMAGEJ they >> are now grey. Furthermore, when I open those same files "turned" grey back >> in image they are now grey instead of being their original color (blue red >> or green). Can someone please help? Thank you >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: HELP needed from IMAGEJ to Photoshop
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I am not sure, if I understand your question properly.
Please look up (just google it) the usability of LUTs (look-up tables). Unless you record with an RGB camera, usually your images ARE grayscale. For visibility reasons (i.e. looking simultaneously at 2/3 images aka channels), the channels representing different fluorophores are colorized. This is artificial and has absolutely no relevance. When you save your ImageJ image with three DIFFERENT channels as tiff, it is saved as multilayer tiff. I dont know what to do with that in Photoshop, but a wild guess would be to work on the layer concept, put each channel in a separate layer and apply the color (aka Lookup) you want. Surely, it would be better to convert your image to RGB in ImageJ and then save it. Again, my guess would be that the splitting operation in photoshop would now represent the proper colors, given that you had R,G and B as separate channels in the original image. If you had cyan, magenta and yellow, then a RGB split would not work. Maybe my answer provided some keywords that help you to look further. cheers, Johannes *Dr. Johannes Koch* *Tissue Med Biosciences GmbH* Magnesitstrasse1 | A-3500 Krems T: +43/2732/87470-300 | M: [hidden email] <mailto:[hidden email]> *www.tmbiosciences.com <http://www.tmbiosciences.com/>* Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Information. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte unverzüglich den Absender und vernichten Sie diese E-Mail sofort. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser E-Mail sind nicht gestattet. This e-mail may contain confidential and/or privileged information. If you are not the intended recipient or have received this e-mail in error please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. Am 28.08.2013 09:33, schrieb Duleep Samuel: > if you can save as jpg in ImageJ then photoshop will open in color,Samuel, > Bangalore, India > > > On Wed, Aug 28, 2013 at 12:53 PM, Dionysios Lefkaditis <[hidden email] >> wrote: >> Hi balloo02, >> >> While I am not a Photoshop user, I am pretty sure that what you are seeing >> is correct. I will try to give you an answer in simple words. When you >> split an image into its colour channels, they essentially become single >> channel (greyscale) images. So when opening them in Photoshop, there is no >> way that that application knows that the image opened used to be a colour >> component of colour image. Are the images identical to each other, or they >> are slightly different? Of course that heavily depends on what was your >> original image. Try to merge the colour channel images back to a colour >> image and check if that will give you your original image. Hope that >> helps... >> >> cheers! >> >> >> On Wed 28 Aug 2013 04:36:05 AM CEST, balloo02 . wrote: >> >>> Hi, I am in dire need of help with converting imagej files that are saved >>> as TIFF files to viewing them in Photoshop. In IMAGEJ, my images have 3 >>> separate channels (blue, red, green). My problem is that when I view the >>> split images in photoshop they are gre,. Instead of my split images >>> being >>> blue, red, or green like when I saved them as TIFF files from IMAGEJ they >>> are now grey. Furthermore, when I open those same files "turned" grey back >>> in image they are now grey instead of being their original color (blue red >>> or green). Can someone please help? Thank you >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> >>> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> >> > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: HELP needed from IMAGEJ to Photoshop
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It's easiest to convert your image to RGB in Image J. It would likely go
fastest. But if it is a fluorescence image, and you want to convert in Photoshop, you can do that in 2 steps: 1. Convert to RGB Color (Image> Mode> RGB Color) 2. In the Levels dialog box, make the two channels you *don't* want to a level of zero (0). For example, if you want the grayscale image to be Red, under Image > Adjustment > Levels, in the Levels dialog box, click on the Channels drop down and choose the Green channel. In the Output Levels portion of the dialog box (the bottommost slider), type "0" into the right hand box. Then do the same with the Blue channel. This will leave you with red. If you record an action (macro) while doing this, you can assign an F key, and then hit the F key to do this to all other images. This can be done in the Actions palette (Window > Actions). Or you can make what is called a droplet (File > Automate > Create Droplet). You can create a droplet, put it on your desktop, and then drag all pertinent images into it to batch this action. Photoshop is worth using when automating functions. Good luck! Jerry On Wed, Aug 28, 2013 at 6:43 AM, Johannes Koch <[hidden email]> wrote: > I am not sure, if I understand your question properly. > > Please look up (just google it) the usability of LUTs (look-up tables). > Unless you record with an RGB camera, usually your images ARE grayscale. > For visibility reasons (i.e. looking simultaneously at 2/3 images aka > channels), the channels representing different fluorophores are colorized. > This is artificial and has absolutely no relevance. > > When you save your ImageJ image with three DIFFERENT channels as tiff, it > is saved as multilayer tiff. I dont know what to do with that in Photoshop, > but a wild guess would be to work on the layer concept, put each channel in > a separate layer and apply the color (aka Lookup) you want. > > Surely, it would be better to convert your image to RGB in ImageJ and then > save it. Again, my guess would be that the splitting operation in photoshop > would now represent the proper colors, given that you had R,G and B as > separate channels in the original image. If you had cyan, magenta and > yellow, then a RGB split would not work. > > Maybe my answer provided some keywords that help you to look further. > > cheers, > Johannes > > > > > *Dr. Johannes Koch* > > *Tissue Med Biosciences GmbH* > > Magnesitstrasse1 | A-3500 Krems > > T: +43/2732/87470-300 | M: [hidden email] <mailto: > [hidden email]> > > *www.tmbiosciences.com <http://www.tmbiosciences.com/**>* > > Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte > Information. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail > irrtümlich erhalten haben, informieren Sie bitte unverzüglich den Absender > und vernichten Sie diese E-Mail sofort. Das unerlaubte Kopieren sowie die > unbefugte Weitergabe dieser E-Mail sind nicht gestattet. > > This e-mail may contain confidential and/or privileged information. If you > are not the intended recipient or have received this e-mail in error please > notify the sender immediately and destroy this e-mail. Any unauthorized > copying, disclosure or distribution of the material in this e-mail is > strictly forbidden. > > Am 28.08.2013 09:33, schrieb Duleep Samuel: > > if you can save as jpg in ImageJ then photoshop will open in color,Samuel, >> Bangalore, India >> >> >> On Wed, Aug 28, 2013 at 12:53 PM, Dionysios Lefkaditis < >> [hidden email] >> >>> wrote: >>> Hi balloo02, >>> >>> While I am not a Photoshop user, I am pretty sure that what you are >>> seeing >>> is correct. I will try to give you an answer in simple words. When you >>> split an image into its colour channels, they essentially become single >>> channel (greyscale) images. So when opening them in Photoshop, there is >>> no >>> way that that application knows that the image opened used to be a colour >>> component of colour image. Are the images identical to each other, or >>> they >>> are slightly different? Of course that heavily depends on what was your >>> original image. Try to merge the colour channel images back to a colour >>> image and check if that will give you your original image. Hope that >>> helps... >>> >>> cheers! >>> >>> >>> On Wed 28 Aug 2013 04:36:05 AM CEST, balloo02 . wrote: >>> >>> Hi, I am in dire need of help with converting imagej files that are >>>> saved >>>> as TIFF files to viewing them in Photoshop. In IMAGEJ, my images have 3 >>>> separate channels (blue, red, green). My problem is that when I view the >>>> split images in photoshop they are gre,. Instead of my split images >>>> being >>>> blue, red, or green like when I saved them as TIFF files from IMAGEJ >>>> they >>>> are now grey. Furthermore, when I open those same files "turned" grey >>>> back >>>> in image they are now grey instead of being their original color (blue >>>> red >>>> or green). Can someone please help? Thank you >>>> >>>> -- >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html> >>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html> >>>> > >>>> >>>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html> >>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html> >>> > >>> >>> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> >> >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> > -- Jerry (Gerald) Sedgewick quickphotoshop.com http://www.imagingandanalysis.com Author: "Scientific Imaging with Photoshop: Methods, Measurement and Ouput" Automated Image Measurement services and systems; On-Site and on-line training for image acquisition/processing/quantitation in science, microscopy and medicine. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: HELP needed from IMAGEJ to Photoshop
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In reply to this post by balloo02 .
HI Balloo,
I assume that in ImageJ you have applied a colour Look Up Table (LUT). These images should still open correctly in Photoshop if they are 8 bit colour. However, try converting your images to RGB (Image - Type - RGB Color) and save them as TIFF as mentioned by Johannes in his post. They should then open in Photoshop in colour. Kind regards, Jacqui Jacqueline Ross Biomedical Imaging Microscopist Biomedical Imaging Research Unit School of Medical Sciences Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Tel: 64 9 923 7438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of balloo02 . Sent: Wednesday, 28 August 2013 2:36 p.m. To: [hidden email] Subject: HELP needed from IMAGEJ to Photoshop Hi, I am in dire need of help with converting imagej files that are saved as TIFF files to viewing them in Photoshop. In IMAGEJ, my images have 3 separate channels (blue, red, green). My problem is that when I view the split images in photoshop they are gre,. Instead of my split images being blue, red, or green like when I saved them as TIFF files from IMAGEJ they are now grey. Furthermore, when I open those same files "turned" grey back in image they are now grey instead of being their original color (blue red or green). Can someone please help? Thank you -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by balloo02 .
Dear balloon02,
On Tue, 27 Aug 2013, balloo02 . wrote: > Hi, I am in dire need of help with converting imagej files that are > saved as TIFF files to viewing them in Photoshop. In IMAGEJ, my images > have 3 separate channels (blue, red, green). My problem is that when I > view the split images in photoshop they are gre,. Instead of my split > images being blue, red, or green like when I saved them as TIFF files > from IMAGEJ they are now grey. Furthermore, when I open those same files > "turned" grey back in image they are now grey instead of being their > original color (blue red or green). Can someone please help? Thank you Please note that the red/green/blue visualization of scientific images is just a compromise, mostly for historical reasons. Scientific images are usually multi-channel, and visualizing them as RGB is actually wrong: imagine an image of green fluorescent cells, the first channel representing a range of wavelengths -- smooshing them all into the same green is obiously incorrect, I hope you agree. Worse: the vast majority of computer screens is not calibrated, so it depends on the screen *which* wrong green you see. Further, the pixel values stored in scientific images are typically *not* intensities as in photographs. See http://www.4p8.com/eric.brasseur/gamma.html for the very real implications of this issue. And then there is also the issue of human vision: our color vision is simply not very precise (as you can easily verify yourself at dusk: you see gray with only minimal color). Assuming that you want to present your multi-channel data to others, I would therefore *strongly* suggest to keep the images in grayscale, but color their labels. That way, you have a clear representation with minimal information loss. Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: HELP needed from IMAGEJ to Photoshop
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Lots of interesting (and perhaps debatable points), but I think this response misses the main point.
The OP has an RGB image and exports it in TIFF. He is confused when he views the individual channels and Photoshop displays them as gray-scale. The answer is: when you split the RGB image into three separate 1-channel images, you no longer have "color" images. Each individual channel is a scalar image, which Photoshop will display as gray-scale, by default. If you want to display the R channel as a collection of shades of red, then you need to either: a) export 3 RGB images - after first ZEROING the channels you don't want to see. ZEROING the (say) G and B channels is not the same as REMOVING them. REMOVING the G and B channels gives you a gray-scale image. ZEROing those channels gives you an RGB image where all of the colors are shades of R OR… b) use Photoshop tools (sorry, my fingers don't do Photoshop so I can't give specific button pushes - but I'm sure this is easy) to convert each 1-channel image back into a color image. One perfectly reasonable way to do that is to define a Color LUT that converts scalars to colors. Use one LUT to make the R channel RED, another to make the B channel BLUE, and a third to make the G channel GREEN. This may only be feasible if you have 8-bit images. [aside: nearly 40 years ago I was happily doing all of this with 12-bit LUT's, but then the industry appeared to take a giant step backwards and has only recently started to recover…but I digress] -- Kenneth Sloan [hidden email] On Sep 5, 2013, at 07:03 , Johannes Schindelin <[hidden email]> wrote: > Dear balloon02, > > On Tue, 27 Aug 2013, balloo02 . wrote: > >> Hi, I am in dire need of help with converting imagej files that are >> saved as TIFF files to viewing them in Photoshop. In IMAGEJ, my images >> have 3 separate channels (blue, red, green). My problem is that when I >> view the split images in photoshop they are gre,. Instead of my split >> images being blue, red, or green like when I saved them as TIFF files >> from IMAGEJ they are now grey. Furthermore, when I open those same files >> "turned" grey back in image they are now grey instead of being their >> original color (blue red or green). Can someone please help? Thank you > > Please note that the red/green/blue visualization of scientific images is > just a compromise, mostly for historical reasons. Scientific images are > usually multi-channel, and visualizing them as RGB is actually wrong: > imagine an image of green fluorescent cells, the first channel > representing a range of wavelengths -- smooshing them all into the same > green is obiously incorrect, I hope you agree. Worse: the vast majority of > computer screens is not calibrated, so it depends on the screen *which* > wrong green you see. > > Further, the pixel values stored in scientific images are typically *not* > intensities as in photographs. See > http://www.4p8.com/eric.brasseur/gamma.html for the very real implications > of this issue. > > And then there is also the issue of human vision: our color vision is > simply not very precise (as you can easily verify yourself at dusk: you > see gray with only minimal color). > > Assuming that you want to present your multi-channel data to others, I > would therefore *strongly* suggest to keep the images in grayscale, but > color their labels. That way, you have a clear representation with minimal > information loss. > > Ciao, > Johannes > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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