remote instrumentation for microscopic imaging
Locked
 
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zhong wang |
remote instrumentation for microscopic imaging
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My name is Zhong Wang working for the Bio-Imaging Facility at the Hunter
College, CUNY. At present we are working on a remote instrumentation project for microscopic imaging. This project aims at manipulating microscopic systems from remote sites via the fast internet connection and supporting web conferencing software. By using proper remote connection protocols, microscopic imaging system can be shared remotely for research purposes. Now we are looking for partners to set up networks for tests and demos. The description of our facility can be found from the following link: Bio-Imaging Facility: http://sonhouse.hunter.cuny.edu/fty_view.asp?id=3 If you are interested, please send me an email including: Contact information Job description Your interest Scientific Equipment that can be shared Internet Connection speed Does the remote end have any video conferencing codes? Thank you. Zhong Wang Bio-imaging Facility Hunter College of CUNY email: [hidden email] |
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Craig Brideau |
Re: remote instrumentation for microscopic imaging
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Well, it isn't pretty, but around here we use windows remote desktop sometimes to run our equipment externally. I'm guessing you are looking for something more flexible and robust however.
Craig On Thu, Feb 12, 2009 at 10:45 AM, Zhong Wang <[hidden email]> wrote: My name is Zhong Wang working for the Bio-Imaging Facility at the Hunter |
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Richard Harris-6 |
Re: remote instrumentation for microscopic imaging
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Hello Zhong Hitachi High Technologies markets a system called WAM –
Wide Area Microscopy from Quartz/PCI. When we set up the Imaging Module
here we ‘auditioned’ many systems which made claims of remote instrument
operation capabilities but in demonstrations WAM was the only system that
actually worked out of the box. We have installed WAM on several
instrument including our Zeiss Duo confocal, Zeiss Z1 Imager and our Hitachi
S-3400N SEM and have had great success with remote operations. Rick, From: Confocal Microscopy
List [mailto:[hidden email]] On Behalf Of Craig
Brideau Well, it isn't pretty, but
around here we use windows remote desktop sometimes to run our equipment
externally. I'm guessing you are looking for something more flexible and
robust however. On Thu, Feb 12, 2009 at 10:45 AM, Zhong Wang <[hidden email]>
wrote: My name is Zhong Wang working for the Bio-Imaging Facility
at the Hunter |
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Michelle Peckham |
How do you get the greyscale values out of a colour image into a text file?
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Someone here was asking me about analysing a ‘RAW’ file for colour information, and the simplest way to do what she wants would be to extract the grey scale values out for the red, green and blue channels, and analyse them in a spread sheet. Does anyone know how to do this? Michelle |
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Hi Michelle,
I'd suggest taking the spilt files into imageJ and then saving them as text files. - as simple as that! Open the RAW file, go to image->color->RGB split, and then save each as a text file. Hope this helps Neil Date: Fri, 13 Feb 2009 15:31:07 +0000 From: [hidden email] Subject: How do you get the greyscale values out of a colour image into a text file? To: [hidden email] Someone here was asking me about analysing a ‘RAW’ file for colour information, and the simplest way to do what she wants would be to extract the grey scale values out for the red, green and blue channels, and analyse them in a spread sheet. Does anyone know how to do this? Michelle Beyond Hotmail — see what else you can do with Windows Live Find out more! |
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Michelle Peckham |
Re: How do you get the greyscale values out of a colour image into a text file?
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I thought you might be able to do something like this – but hadn’t had a chance to try it! That’s great. Michelle On 13/02/2009 16:06, "Neil Kad" <nkaddy@...> wrote: Hi Michelle, |
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Chris Tully |
Re: How do you get the greyscale values out of a colour image into a text file?
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In reply to this post by Michelle Peckham
Michelle,
You may want to check out the color correction and measurement facilities in Image-Pro Plus (http://www.mediacy.com). Although I no longer work for the company, I was involved in the development and testing of these tools. I am recommending this because in my experience most people who feel that they need to work directly with the pixel intensity values really don't understand digital images and/or what they are trying get out of the image. Usually a few minutes working with a specialist in image processing and analysis can reveal tools and methods that achieve the desired results with far less effort. Working directly with pixel intensity values is neither easy or fast! This is why both commercial and free programs for image analysis have been developed. -Chris Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-888-1021 http://www.linkedin.com/in/christully On Fri, Feb 13, 2009 at 10:31 AM, Michelle Peckham <[hidden email]> wrote: > A little bit off the topic, but > > Someone here was asking me about analysing a 'RAW' file for colour > information, and the simplest way to do what she wants would be to extract > the grey scale values out for the red, green and blue channels, and analyse > them in a spread sheet. > > Does anyone know how to do this? > > Michelle |
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Jerry Sedgewick-2 |
Re: How do you get the greyscale values out of a colour image into a text file?
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In reply to this post by Michelle Peckham
Is the file in the Raw format, such as those generated by Nikon and
Canon consumer cameras? Or did you mean that the person was asking about the original (unaltered or raw) file? If it is the Nikon or Canon Raw format, then it was derived from a mosaic chip and colors will have to be assigned to each pixel through some kind of conversion "engine." Photoshop uses its own Adobe Camera Raw (ACR) engine in all the CS versions (as I recall). If the lighting for the study was consistent, and if the study occurred over more than one imaging session, then the settings in Adobe Camera Raw should be set similarly for the experiment, or the colors will have to be adjusted by using a reference standard (such as a neutral gray card, Macbeth color chart, or some consistent part of the specimen that is white or gray). If the colors are not assigned or adjusted to a standard, then the colors will be inconsistent from session to session. Canon and Nikon both have proprietary engines in which colors are generated at each x, y position. These can also be used, but make sure the gamma is set to 1, and, again, adjust colors based upon reference standards if images were taken at more than one session. Before opening the image in Photoshop, the Color Settings in the menu (Preferences>Color Settings) are changed from the RGB default setting (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the gamma at 1 (no alteration of post-ACR values). This color setting can be downloaded from quickphotoshop.com, but make sure to click on Book: Supplemental Info (not Download). Photoshop changes the gamma when using any of the other color settings. Gamma is a reference to the adjustment of pixel values destined for display on a computer monitor in which the Greek symbol gamma is the exponent in a math formula. Once in Photoshop, in the menu, under Windows, choose Channels (Windows>Channels). In the Channels palette, click on the upper right arrowhead and choose Split Channels from the drop down list. This will separate the red, green and blue channels for subsequent measurement. In the distant past, I believe I used Image J to generate pixel values at each x, y position, but maybe it was MatLab or MetaMorph. Maybe another person on the list can add that information. Cheers! Michelle Peckham wrote: > A little bit off the topic, but > > Someone here was asking me about analysing a ‘RAW’ file for colour > information, and the simplest way to do what she wants would be to > extract the grey scale values out for the red, green and blue > channels, and analyse them in a spread sheet. > > Does anyone know how to do this? > > Michelle -- Jerry (Gerald) Sedgewick Program Director, Biomedical Image Processing Lab (BIPL) Department of Neuroscience, University of Minnesota 312 Church St. SE, 1-205 Hasselmo Hall Minneapolis, MN 55455 (612) 624-6607 [hidden email] http://www.bipl.umn.edu Author: "Scientific Imaging with Photoshop: Methods, Measurement and Output." Rawlight.com (dba Sedgewick Initiatives) 965 Cromwell Avenue Saint Paul, MN 55114 [hidden email] (651) 308-1466 http://www.quickphotoshop.com http://www.heartFROMstone.com http://www.rawlight.com --- Get FREE High Speed Internet from USFamily.Net! -- http://www.usfamily.net/mkt-freepromo.html --- |
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Michelle Peckham |
Re: How do you get the greyscale values out of a colour image into a text file?
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Thanks Jerry
These are pictures taken with a digital camera (i.e. Nikon or Canon) in 'raw' format. So your advice is great. This person wants to work out how much area is a particular shade/hue, so we thought grey scale numbers in R,G and B channels would be the thing to go for. So thanks for this. Michelle On 13/02/2009 16:46, "Jerry Sedgewick" <[hidden email]> wrote: > Is the file in the Raw format, such as those generated by Nikon and > Canon consumer cameras? Or did you mean that the person was asking about > the original (unaltered or raw) file? > > If it is the Nikon or Canon Raw format, then it was derived from a > mosaic chip and colors will have to be assigned to each pixel through > some kind of conversion "engine." Photoshop uses its own Adobe Camera > Raw (ACR) engine in all the CS versions (as I recall). If the lighting > for the study was consistent, and if the study occurred over more than > one imaging session, then the settings in Adobe Camera Raw should be set > similarly for the experiment, or the colors will have to be adjusted by > using a reference standard (such as a neutral gray card, Macbeth color > chart, or some consistent part of the specimen that is white or gray). > If the colors are not assigned or adjusted to a standard, then the > colors will be inconsistent from session to session. > > Canon and Nikon both have proprietary engines in which colors are > generated at each x, y position. These can also be used, but make sure > the gamma is set to 1, and, again, adjust colors based upon reference > standards if images were taken at more than one session. > > Before opening the image in Photoshop, the Color Settings in the menu > (Preferences>Color Settings) are changed from the RGB default setting > (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the > gamma at 1 (no alteration of post-ACR values). This color setting can be > downloaded from quickphotoshop.com, but make sure to click on Book: > Supplemental Info (not Download). Photoshop changes the gamma when using > any of the other color settings. Gamma is a reference to the adjustment > of pixel values destined for display on a computer monitor in which the > Greek symbol gamma is the exponent in a math formula. > > Once in Photoshop, in the menu, under Windows, choose Channels > (Windows>Channels). In the Channels palette, click on the upper right > arrowhead and choose Split Channels from the drop down list. This will > separate the red, green and blue channels for subsequent measurement. > > In the distant past, I believe I used Image J to generate pixel values > at each x, y position, but maybe it was MatLab or MetaMorph. Maybe > another person on the list can add that information. > > Cheers! > > > > Michelle Peckham wrote: >> A little bit off the topic, but >> >> Someone here was asking me about analysing a RAW¹ file for colour >> information, and the simplest way to do what she wants would be to >> extract the grey scale values out for the red, green and blue >> channels, and analyse them in a spread sheet. >> >> Does anyone know how to do this? >> >> Michelle > |
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Chris Tully |
Re: How do you get the greyscale values out of a colour image into a text file?
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Michelle,
Not to be to commercial here but the kind of question you are asking here is trivial to answer in most image analysis programs without dropping down to the individual pixel values. Since you are using a single chip color camera keep in mind that some fraction of the pixels in each channel is extrapolated from its neighbors (For a Bayer pattern chip, 75% of the red and blue and 50% or the green pixels are extrapolated from their neighbors!). Assuming that you are talking about "consumer" type digital cameras, I am not as familiar with the chips and filter patterns that they use. Please note that on all the "consumer" grade digital cameras I have used, the "raw" format simply means an uncompressed image (usually in TIFF format). It does not mean the same thing as "raw" means coming from a "scientific" digital camera which usually means a gray scale image exactly as it was extracted from the chip before color processing (interpolation). Taking the software that I am most familiar with as an example (Image-Pro Plus) it is simple, even automatable, to select the range of Red, Green and Blue values of interest and ask the software for anything from the number of objects that meet that threshold to the total number of pixels that meet that threshold. If you have access to a copy of Image-Pro Plus, I would be happy to guide you through the analysis by phone or email. Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-888-1021 http://www.linkedin.com/in/christully On Fri, Feb 13, 2009 at 11:51 AM, Michelle Peckham <[hidden email]> wrote: > Thanks Jerry > > These are pictures taken with a digital camera (i.e. Nikon or Canon) in > 'raw' format. So your advice is great. > > This person wants to work out how much area is a particular shade/hue, so we > thought grey scale numbers in R,G and B channels would be the thing to go > for. > > So thanks for this. > > Michelle > > > On 13/02/2009 16:46, "Jerry Sedgewick" <[hidden email]> wrote: > >> Is the file in the Raw format, such as those generated by Nikon and >> Canon consumer cameras? Or did you mean that the person was asking about >> the original (unaltered or raw) file? >> >> If it is the Nikon or Canon Raw format, then it was derived from a >> mosaic chip and colors will have to be assigned to each pixel through >> some kind of conversion "engine." Photoshop uses its own Adobe Camera >> Raw (ACR) engine in all the CS versions (as I recall). If the lighting >> for the study was consistent, and if the study occurred over more than >> one imaging session, then the settings in Adobe Camera Raw should be set >> similarly for the experiment, or the colors will have to be adjusted by >> using a reference standard (such as a neutral gray card, Macbeth color >> chart, or some consistent part of the specimen that is white or gray). >> If the colors are not assigned or adjusted to a standard, then the >> colors will be inconsistent from session to session. >> >> Canon and Nikon both have proprietary engines in which colors are >> generated at each x, y position. These can also be used, but make sure >> the gamma is set to 1, and, again, adjust colors based upon reference >> standards if images were taken at more than one session. >> >> Before opening the image in Photoshop, the Color Settings in the menu >> (Preferences>Color Settings) are changed from the RGB default setting >> (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the >> gamma at 1 (no alteration of post-ACR values). This color setting can be >> downloaded from quickphotoshop.com, but make sure to click on Book: >> Supplemental Info (not Download). Photoshop changes the gamma when using >> any of the other color settings. Gamma is a reference to the adjustment >> of pixel values destined for display on a computer monitor in which the >> Greek symbol gamma is the exponent in a math formula. >> >> Once in Photoshop, in the menu, under Windows, choose Channels >> (Windows>Channels). In the Channels palette, click on the upper right >> arrowhead and choose Split Channels from the drop down list. This will >> separate the red, green and blue channels for subsequent measurement. >> >> In the distant past, I believe I used Image J to generate pixel values >> at each x, y position, but maybe it was MatLab or MetaMorph. Maybe >> another person on the list can add that information. >> >> Cheers! >> >> >> >> Michelle Peckham wrote: >>> A little bit off the topic, but >>> >>> Someone here was asking me about analysing a ŒRAW¹ file for colour >>> information, and the simplest way to do what she wants would be to >>> extract the grey scale values out for the red, green and blue >>> channels, and analyse them in a spread sheet. >>> >>> Does anyone know how to do this? >>> >>> Michelle >> > |
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Mark Cannell |
Re: How do you get the greyscale values out of a colour image into a text file?
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As far as Canon is concerned the raw files contain raw sensor data as
well a lot of other info... Here is a link: http://lclevy.free.fr/cr2/ Cheers Mark Chris Tully wrote: > Michelle, > > Not to be to commercial here but the kind of question you are asking > here is trivial to answer in most image analysis programs without > dropping down to the individual pixel values. Since you are using a > single chip color camera keep in mind that some fraction of the pixels > in each channel is extrapolated from its neighbors (For a Bayer > pattern chip, 75% of the red and blue and 50% or the green pixels are > extrapolated from their neighbors!). Assuming that you are talking > about "consumer" type digital cameras, I am not as familiar with the > chips and filter patterns that they use. Please note that on all the > "consumer" grade digital cameras I have used, the "raw" format simply > means an uncompressed image (usually in TIFF format). It does not > mean the same thing as "raw" means coming from a "scientific" digital > camera which usually means a gray scale image exactly as it was > extracted from the chip before color processing (interpolation). > > Taking the software that I am most familiar with as an example > (Image-Pro Plus) it is simple, even automatable, to select the range > of Red, Green and Blue values of interest and ask the software for > anything from the number of objects that meet that threshold to the > total number of pixels that meet that threshold. If you have access > to a copy of Image-Pro Plus, I would be happy to guide you through the > analysis by phone or email. > > Chris Tully > Microscopy and Image Analysis Expert > [hidden email] > 240-888-1021 > http://www.linkedin.com/in/christully > > > > On Fri, Feb 13, 2009 at 11:51 AM, Michelle Peckham > <[hidden email]> wrote: > >> Thanks Jerry >> >> These are pictures taken with a digital camera (i.e. Nikon or Canon) in >> 'raw' format. So your advice is great. >> >> This person wants to work out how much area is a particular shade/hue, so we >> thought grey scale numbers in R,G and B channels would be the thing to go >> for. >> >> So thanks for this. >> >> Michelle >> >> >> On 13/02/2009 16:46, "Jerry Sedgewick" <[hidden email]> wrote: >> >> >>> Is the file in the Raw format, such as those generated by Nikon and >>> Canon consumer cameras? Or did you mean that the person was asking about >>> the original (unaltered or raw) file? >>> >>> If it is the Nikon or Canon Raw format, then it was derived from a >>> mosaic chip and colors will have to be assigned to each pixel through >>> some kind of conversion "engine." Photoshop uses its own Adobe Camera >>> Raw (ACR) engine in all the CS versions (as I recall). If the lighting >>> for the study was consistent, and if the study occurred over more than >>> one imaging session, then the settings in Adobe Camera Raw should be set >>> similarly for the experiment, or the colors will have to be adjusted by >>> using a reference standard (such as a neutral gray card, Macbeth color >>> chart, or some consistent part of the specimen that is white or gray). >>> If the colors are not assigned or adjusted to a standard, then the >>> colors will be inconsistent from session to session. >>> >>> Canon and Nikon both have proprietary engines in which colors are >>> generated at each x, y position. These can also be used, but make sure >>> the gamma is set to 1, and, again, adjust colors based upon reference >>> standards if images were taken at more than one session. >>> >>> Before opening the image in Photoshop, the Color Settings in the menu >>> (Preferences>Color Settings) are changed from the RGB default setting >>> (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the >>> gamma at 1 (no alteration of post-ACR values). This color setting can be >>> downloaded from quickphotoshop.com, but make sure to click on Book: >>> Supplemental Info (not Download). Photoshop changes the gamma when using >>> any of the other color settings. Gamma is a reference to the adjustment >>> of pixel values destined for display on a computer monitor in which the >>> Greek symbol gamma is the exponent in a math formula. >>> >>> Once in Photoshop, in the menu, under Windows, choose Channels >>> (Windows>Channels). In the Channels palette, click on the upper right >>> arrowhead and choose Split Channels from the drop down list. This will >>> separate the red, green and blue channels for subsequent measurement. >>> >>> In the distant past, I believe I used Image J to generate pixel values >>> at each x, y position, but maybe it was MatLab or MetaMorph. Maybe >>> another person on the list can add that information. >>> >>> Cheers! >>> >>> >>> >>> Michelle Peckham wrote: >>> >>>> A little bit off the topic, but >>>> >>>> Someone here was asking me about analysing a ŒRAW¹ file for colour >>>> information, and the simplest way to do what she wants would be to >>>> extract the grey scale values out for the red, green and blue >>>> channels, and analyse them in a spread sheet. >>>> >>>> Does anyone know how to do this? >>>> >>>> Michelle >>>> |
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Sudipta Maiti |
Fluorescence 2009: last day to submit your abstract
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Dear Confocalists,
I remind you about Fluorescence 2009 that we are organizing in Mumbai from March 16-19, 2009. Today is the last date for submitting your abstract. Though it covers all of "biological fluorescence", there is a heavy presence of imaging guys in the conference. Check out www.fluorescence2009.org for the list of speakers. Hope to see you in Mumbai next month. Sudipta maiti On Mon, 16 Feb 2009 12:52:00 +1300, Mark Cannell wrote > As far as Canon is concerned the raw files contain raw sensor data > as well a lot of other info... Here is a link: > > http://lclevy.free.fr/cr2/ > > Cheers Mark > > Chris Tully wrote: > > Michelle, > > > > Not to be to commercial here but the kind of question you are asking > > here is trivial to answer in most image analysis programs without > > dropping down to the individual pixel values. Since you are using a > > single chip color camera keep in mind that some fraction of the pixels > > in each channel is extrapolated from its neighbors (For a Bayer > > pattern chip, 75% of the red and blue and 50% or the green pixels are > > extrapolated from their neighbors!). Assuming that you are talking > > about "consumer" type digital cameras, I am not as familiar with the > > chips and filter patterns that they use. Please note that on all the > > "consumer" grade digital cameras I have used, the "raw" format simply > > means an uncompressed image (usually in TIFF format). It does not > > mean the same thing as "raw" means coming from a "scientific" digital > > camera which usually means a gray scale image exactly as it was > > extracted from the chip before color processing (interpolation). > > > > Taking the software that I am most familiar with as an example > > (Image-Pro Plus) it is simple, even automatable, to select the range > > of Red, Green and Blue values of interest and ask the software for > > anything from the number of objects that meet that threshold to the > > total number of pixels that meet that threshold. If you have access > > to a copy of Image-Pro Plus, I would be happy to guide you through the > > analysis by phone or email. > > > > Chris Tully > > Microscopy and Image Analysis Expert > > [hidden email] > > 240-888-1021 > > http://www.linkedin.com/in/christully > > > > > > > > On Fri, Feb 13, 2009 at 11:51 AM, Michelle Peckham > > <[hidden email]> wrote: > > > >> Thanks Jerry > >> > >> These are pictures taken with a digital camera (i.e. Nikon or Canon) in > >> 'raw' format. So your advice is great. > >> > >> This person wants to work out how much area is a particular shade/hue, > >> thought grey scale numbers in R,G and B channels would be the thing to go > >> for. > >> > >> So thanks for this. > >> > >> Michelle > >> > >> > >> On 13/02/2009 16:46, "Jerry Sedgewick" <[hidden email]> wrote: > >> > >> > >>> Is the file in the Raw format, such as those generated by Nikon and > >>> Canon consumer cameras? Or did you mean that the person was asking > >>> the original (unaltered or raw) file? > >>> > >>> If it is the Nikon or Canon Raw format, then it was derived from a > >>> mosaic chip and colors will have to be assigned to each pixel through > >>> some kind of conversion "engine." Photoshop uses its own Adobe Camera > >>> Raw (ACR) engine in all the CS versions (as I recall). If the lighting > >>> for the study was consistent, and if the study occurred over more than > >>> one imaging session, then the settings in Adobe Camera Raw should be set > >>> similarly for the experiment, or the colors will have to be adjusted by > >>> using a reference standard (such as a neutral gray card, Macbeth color > >>> chart, or some consistent part of the specimen that is white or gray). > >>> If the colors are not assigned or adjusted to a standard, then the > >>> colors will be inconsistent from session to session. > >>> > >>> Canon and Nikon both have proprietary engines in which colors are > >>> generated at each x, y position. These can also be used, but make sure > >>> the gamma is set to 1, and, again, adjust colors based upon reference > >>> standards if images were taken at more than one session. > >>> > >>> Before opening the image in Photoshop, the Color Settings in the menu > >>> (Preferences>Color Settings) are changed from the RGB default setting > >>> (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the > >>> gamma at 1 (no alteration of post-ACR values). This color setting can > >>> downloaded from quickphotoshop.com, but make sure to click on Book: > >>> Supplemental Info (not Download). Photoshop changes the gamma when using > >>> any of the other color settings. Gamma is a reference to the adjustment > >>> of pixel values destined for display on a computer monitor in which the > >>> Greek symbol gamma is the exponent in a math formula. > >>> > >>> Once in Photoshop, in the menu, under Windows, choose Channels > >>> (Windows>Channels). In the Channels palette, click on the upper right > >>> arrowhead and choose Split Channels from the drop down list. This will > >>> separate the red, green and blue channels for subsequent measurement. > >>> > >>> In the distant past, I believe I used Image J to generate pixel values > >>> at each x, y position, but maybe it was MatLab or MetaMorph. Maybe > >>> another person on the list can add that information. > >>> > >>> Cheers! > >>> > >>> > >>> > >>> Michelle Peckham wrote: > >>> > >>>> A little bit off the topic, but > >>>> > >>>> Someone here was asking me about analysing a [WINDOWS-1252?]RAW¹ > >>>> information, and the simplest way to do what she wants would be to > >>>> extract the grey scale values out for the red, green and blue > >>>> channels, and analyse them in a spread sheet. > >>>> > >>>> Does anyone know how to do this? > >>>> > >>>> Michelle > >>>> Dr. Sudipta Maiti Associate Professor Dept. of Chemical Sciences Tata Institute of Fundamental Research Homi Bhabha Raod, Colaba, Mumbai 400005 Ph. 91-22-2278-2716 / 2539 Fax: 91-22-2280-4610 alternate e-mail: [hidden email] url: www.tifr.res.in/~biophotonics |
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Ricardo Figueroa |
Re: How do you get the greyscale values out of a colour image into a text file?
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In reply to this post by Michelle Peckham
If hue or saturation is what you are interested in consider using HSL or
HSV colour space. Converting the corectly registerd RGB images to this is simple and available in most image editing softwares Photoshop, Gimp, and ImageJ all have functions for this. Then finding the area of a certain hue or saturation is a simple mater of thresholding the channel of interest and measuring the resulting area. /Ricardo Figueroa Michelle Peckham wrote: > Thanks Jerry > > These are pictures taken with a digital camera (i.e. Nikon or Canon) in > 'raw' format. So your advice is great. > > This person wants to work out how much area is a particular shade/hue, so we > thought grey scale numbers in R,G and B channels would be the thing to go > for. > > So thanks for this. > > Michelle > > > On 13/02/2009 16:46, "Jerry Sedgewick" <[hidden email]> wrote: > > >> Is the file in the Raw format, such as those generated by Nikon and >> Canon consumer cameras? Or did you mean that the person was asking about >> the original (unaltered or raw) file? >> >> If it is the Nikon or Canon Raw format, then it was derived from a >> mosaic chip and colors will have to be assigned to each pixel through >> some kind of conversion "engine." Photoshop uses its own Adobe Camera >> Raw (ACR) engine in all the CS versions (as I recall). If the lighting >> for the study was consistent, and if the study occurred over more than >> one imaging session, then the settings in Adobe Camera Raw should be set >> similarly for the experiment, or the colors will have to be adjusted by >> using a reference standard (such as a neutral gray card, Macbeth color >> chart, or some consistent part of the specimen that is white or gray). >> If the colors are not assigned or adjusted to a standard, then the >> colors will be inconsistent from session to session. >> >> Canon and Nikon both have proprietary engines in which colors are >> generated at each x, y position. These can also be used, but make sure >> the gamma is set to 1, and, again, adjust colors based upon reference >> standards if images were taken at more than one session. >> >> Before opening the image in Photoshop, the Color Settings in the menu >> (Preferences>Color Settings) are changed from the RGB default setting >> (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the >> gamma at 1 (no alteration of post-ACR values). This color setting can be >> downloaded from quickphotoshop.com, but make sure to click on Book: >> Supplemental Info (not Download). Photoshop changes the gamma when using >> any of the other color settings. Gamma is a reference to the adjustment >> of pixel values destined for display on a computer monitor in which the >> Greek symbol gamma is the exponent in a math formula. >> >> Once in Photoshop, in the menu, under Windows, choose Channels >> (Windows>Channels). In the Channels palette, click on the upper right >> arrowhead and choose Split Channels from the drop down list. This will >> separate the red, green and blue channels for subsequent measurement. >> >> In the distant past, I believe I used Image J to generate pixel values >> at each x, y position, but maybe it was MatLab or MetaMorph. Maybe >> another person on the list can add that information. >> >> Cheers! >> >> >> >> Michelle Peckham wrote: >> >>> A little bit off the topic, but >>> >>> Someone here was asking me about analysing a ŒRAW¹ file for colour >>> information, and the simplest way to do what she wants would be to >>> extract the grey scale values out for the red, green and blue >>> channels, and analyse them in a spread sheet. >>> >>> Does anyone know how to do this? >>> >>> Michelle >>> > > |
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