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ledcolorimaging [2013/10/23 17:22]
kthorn
ledcolorimaging [2013/10/23 12:27] (current)
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 [[https://​github.com/​kthorn/​MatlabMM/​tree/​master|This matlab code]] does this. It makes several assumptions about the data structure, but should work with a little tweaking for most image files. The main code is [[https://​github.com/​kthorn/​MatlabMM/​blob/​master/​RGB_process.m|here]];​ flatfielding is done in a [[https://​github.com/​kthorn/​MatlabMM/​blob/​master/​flatField.m|separate function]]. [[https://​github.com/​kthorn/​MatlabMM/​tree/​master|This matlab code]] does this. It makes several assumptions about the data structure, but should work with a little tweaking for most image files. The main code is [[https://​github.com/​kthorn/​MatlabMM/​blob/​master/​RGB_process.m|here]];​ flatfielding is done in a [[https://​github.com/​kthorn/​MatlabMM/​blob/​master/​flatField.m|separate function]].
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 +However, this image analysis isn't complete - while it will white balance the images, it doesn'​t guarantee that the colors come out looking right. To do this we need to color calibrate the microscope. Unfortunately,​ this isn't a simple process - see for example, the wikipedia pages on [[http://​en.wikipedia.org/​wiki/​Color_calibration|color calibration]] and [[http://​en.wikipedia.org/​wiki/​Color_balance|color balance]] - but we're working on it.
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 +You can see some examples of the results of this RGB imaging at the following links:
 +  * [[http://​nic.ucsf.edu/​blog/?​p=678#​more-678|A blog post I made about this process]]
 +  * [[http://​gigapan.com/​gigapans/​137537|A 2.3 gigapixel image of a spleen section]]
 +  * [[http://​gigapan.com/​gigapans/​141993|A 290 megapixel image of an ovary section]]
/var/www/html/dokuwiki/data/pages/ledcolorimaging.txt · Last modified: 2013/10/23 12:27 (external edit)