# Image Processing-pixel intensity [closed]

Thanks @Ali Hashmi for help I am new to using Mathematica. I haven't come across a post that would answer this issue. I would like to identify the 2 dyes (based on intensity against all the dyes used) which make up each segment. So when I have all the channels in a merged image I can assign each segment a specific pseudocolor for each dye combination. So for example I want to color all segments in the merged image which have channel green and channel blue signals green. Have used the ImageHistogram function but have no idea how to tackle this on an individual segment basis. I have attached only 1 channel and a mask as Im limited to the amount of links I can upload. The mask was formed from the merged image of all the channels to segment into ROIs outside of Mathematica.

## closed as unclear what you're asking by george2079, MarcoB, happy fish, m_goldberg, glSApr 19 '17 at 10:33

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

• if you use ImageData Mathematica will give you a list of tridimensional vectors. Each component rapresent the value of the intensity of a single channel per pixel. By writing Mean@ImageData["imagepath"][[1,1;;5]] the output will be once again a tridimensional vector whose components are the mean of the intensity of each channel in the first line from column1 to 5 – Alucard Feb 28 '17 at 2:22
• For the application of colors to an image, look at the documentation for Colorize. – bill s Feb 28 '17 at 3:46
• voting to close as I think he reposed basically the same thing here: mathematica.stackexchange.com/q/139362/2079 – george2079 Apr 17 '17 at 16:29

lets say you have the following channels: channel1, channel2 and channel3. Provided we have the binarized mask (segmentation of your cell) stored as mask then we can do the following:

intensity1 = ImageMeasurements[channel1,"MeanIntensity", Masking -> mask];


you can do the same for others. Or better map the list of channels as:

{intensity1,intensity2,intensity3} =