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*[[Hosuk:Lab_Notes|LabNote]] ===Pixel-by-Pixel Detection : v1.1=== *Add more functions in normalization and digit assignment *Code **DecodePxPx.m : Main **Info.m : read basic information, parameter setting **Normalize.m : normalize, 1st and 2nd stage… including max. valuse selection, zero call method before 2nd stage normalization **AssignDigit.m : assign 1 (488 channel), 2(Cy3), 3(Cy5) and 0… by max. value then cutout non infomal pixels by looking distribution in 3 axis space in spherical coordinates! **MappingGene.m : map barcodes at each pixel to gene, and clustering and size filtering + watershed segmentation **PlotIntensity.m : Plot pixels with intensity in 3 channels *Assign Digit by spatial filtering *1. Zero call by using threshold cutoff (decided by either fixed value or % from the max) *2. Assign color ID (1:488, 2:Cy3, 3:Cy5) by Max value among 3 normalized intensities *3. Convert to spherical coordinate, and select Pixels within range **488 : 0<= azimuth <=pi/6(30degree), 0<=elevation<=pi/6(30degree) **Cy3 : 2pi/6(60degree)<= azimuth <=pi/2(90degree) , 0<=elevation<=pi/6(30degree) **Cy5 : 2pi/6(60degree)<= elevation <=pi/2(90degree) [[File:Decoding_Result_smallimage_PxPx_v1.1_2015-03-02_3.png|800px]]
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