ledcolorimaging
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ledcolorimaging [2013/10/23 17:22] kthorn |
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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]] | ||
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