I would like to know how many pixels of the scanned flat skin is of every color in order to compare between species. In particular we are studying the color skin differences between Apodemus sylvaticus and A. flavicollis from NE Spain.
In Photoshop there is the "Quick selection tool" that allows you to select pixels of the same color. After you select the areas you want to measure, you press Shift+Control+M and Photoshop will give you a value in pixels, relative to the area you have selected. If you do not have Photoshop, the freeware ImageJ can do the same job. http://rsbweb.nih.gov/ij/
There are many tutorials in the internet and many papers showing methods for what you need, using ImageJ. For example: http://www.med.upenn.edu/cellbio/documents/ImageJ_ColorSegmentpdf.pdf
http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#spatial_measurements
http://www.cas.miamioh.edu/~meicenrd/anatomy/Ch14_IndependentInvestigation/Brief%20Instructions%20for%20ImageJ.html
I think it is better to use reflectane spectra. Later, you can "quantify" color with Montgomerie's CLR (http://post.queensu.ca/~mont/color/analyze.html).
If you just want to measure area, you can use Photoshop or ImageJ.
Thank you Rhainer, but I want a cheap solution, and I guess that you are proposing to use an spectrometer? I am sorry but I am not familiar with this technics. I want to use a scanner to scan the flat fur of the small mammals and use a simple software (someone told me that photoshop can do it but I don't know how) to quantify the number of pixels of every colour in the image.
For our study of scrotal coloration in live vervet monkeys, we used digital photographs with a color scale (taken with a cheap handheld camera) and then analyzed them in Photoshop. Cheap and easy. You can see the methods in the paper on my profile (Danzy et al. 2013).
In Photoshop there is the "Quick selection tool" that allows you to select pixels of the same color. After you select the areas you want to measure, you press Shift+Control+M and Photoshop will give you a value in pixels, relative to the area you have selected. If you do not have Photoshop, the freeware ImageJ can do the same job. http://rsbweb.nih.gov/ij/
There are many tutorials in the internet and many papers showing methods for what you need, using ImageJ. For example: http://www.med.upenn.edu/cellbio/documents/ImageJ_ColorSegmentpdf.pdf
http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#spatial_measurements
http://www.cas.miamioh.edu/~meicenrd/anatomy/Ch14_IndependentInvestigation/Brief%20Instructions%20for%20ImageJ.html
Thank you very much Christopher and Rhainer. I will have a look to the attached papers.
this recently published software helps with the visualization of spectral data http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12069/abstract @hylopsar
Besides previous answers, which probably offer more complete solutions, there is the R package tiff, that allows you to load tiff images and quantify and work with the pixel values of the different image bands.
Carlos Pena, I did not see information in the pdf about functions of background and illumination. Is it customizable or does it have default values?
Thanks Francisco, may be the solution you propose is better for my work. The problem is that I don't know anything about R!!! I downloaded the program long time ago, but I haven't use it yet. But a similar option can be found in Photoshop and ImageJ as Rhainer told us. As I can see these programs only quantify the colours of the Red-Green-Blue, bands.
Hi Ignasi, I can understand that the my proposed solution may seem difficult if you are not familiar with R, but is very worth it. I am confronting a similar problem, I wanted to quantify color but had no access/budget for a spectrometer so I took pictures with a digital camera and had to figure out how to manage that. I used photoshop to crop the pictures, and the tiff package to start analyzing them. The good thing about using R is that when it imports the image you can trasform it into a matrix that allows you to do any statistical analysis that you may need.
Francisco, can you tell me if the R option analyses the colours of the three main colour bands (RGB)?, or it analyses the real colour? I have tried ImageJ and it seems that it calculates the mean number of pixels of the three main colours in a cropped image, and it translates the data into a spreadsheet that can be opened with excel, so it also can be analysed.
Hi Ignasi.
The R option allows you to use each of the three bands as a numeric dataset to which you can do any statistical and mathematical analysis that you could do with any other. In that sense yes, you would be able to work with the real pixel values for each band, but you have to be aware that pixel values from a photograph are just a number between 0 and 250 so the information that you have is not "real color". I hope this helps!
Ignasi, now I see what you really want. In Photoshop, you can get the values for Hue, Brightness and Chroma of specific pixels in RGB and CMYK. With these 3 values, you can get close to what the real color is, and compare them between your species using statistical tests. However, pictures must be taken against a standard background (white paper or a real standard of known spectra, which you can buy in stores), and the values form your samples controlled against the values from this background. BUT...like Francisco said, it is not the best way to measure this, since there is variation in light intensity and the resultant color according to many factors (e.g. the surface structure, angle in relation to the light source, positioning of the sample, sensitivity of the camera to specific wavelengths, optical receptors in the study animal, etc...). For instance, your camera will get images in infrared wavelengths, but probably your animal (and us) cannot see that. Some cameras are not sensitive to UV, although many animals are. Well, you see the point that you will get close to the color, but not the real reflectance spectra. In your study, you may show that the colors in the animals are different, but you cannot show the color of your samples since you won't have this data.
Here are some references that you should follow:
Bergman TJ, Beehner JC (2008) A simple method for measuring colour in wild animals: validation and use on chest patch colour in geladas (Theropithecus gelada). Biol J Linn Soc 94:231–240
Higham JP, Brent LJN, Dubuc C, Accamando AK, Engelhardt A, Gerald MS, Heistermann M, Stevens M (2010) Color signal information content and the eye of the beholder: a case study in the rhesus macaque. Behav Ecol 21:739–746
Thomas W. Pike. Using digital cameras to investigate animal colouration: estimating sensor sensitivity functions. Behavioral Ecology and Sociobiology
April 2011, Volume 65, Issue 4, pp 849-858
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