blogtng:2010-05-04:photobleaching_correction_3d_time_series
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blogtng:2010-05-04:photobleaching_correction_3d_time_series [2010/05/04 10:08] – created kota | blogtng:2010-05-04:photobleaching_correction_3d_time_series [2016/05/24 12:46] (current) – external edit 127.0.0.1 | ||
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Anycase, there should be 3D-t bleach correction tool (and I need it NOW). I might make some quick solution using two methods, one using division of first frame and the other with exponential fitting. | Anycase, there should be 3D-t bleach correction tool (and I need it NOW). I might make some quick solution using two methods, one using division of first frame and the other with exponential fitting. | ||
- | By the way, bleaching corrected images cannot be used for intensity quantification. If you are analyzing shapes or positions, no problem for quantification. | + | By the way, bleaching corrected images cannot |
+ | |||
+ | ---- | ||
+ | |||
+ | here is the " | ||
+ | < | ||
+ | macro " | ||
+ | run(" | ||
+ | getDimensions(width, | ||
+ | if (frames == 1) { | ||
+ | uslices = getNumber(" | ||
+ | if ((slices%uslices) !=0) exit(" | ||
+ | frames = slices / uslices; | ||
+ | } | ||
+ | tIntA = newArray(frames); | ||
+ | setBatchMode(true); | ||
+ | for(i=0; i< | ||
+ | startf = (i*slices)+1; | ||
+ | endf = (i+1)*slices; | ||
+ | op =" | ||
+ | run(" | ||
+ | // | ||
+ | getRawStatistics(nPixels, | ||
+ | if (i==0) tIntA[i] = mean; | ||
+ | else tIntA[i] = mean/ | ||
+ | close(); | ||
+ | } | ||
+ | setBatchMode(" | ||
+ | tIntA[0] =1; | ||
+ | for(i=0; i< | ||
+ | for(j=0; j< | ||
+ | curframe = i*slices + j+1; | ||
+ | setSlice(curframe); | ||
+ | // | ||
+ | op = " | ||
+ | run(" | ||
+ | } | ||
+ | print(" | ||
+ | } | ||
+ | } | ||
+ | |||
+ | </ | ||
+ | |||
+ | ---- | ||
+ | |||
+ | **Before Correction** (each row is a time point, with 8 z-slices)\\ | ||
+ | {{: | ||
+ | Average intensity along stack slices. 5 peaks corresponds to 5 time points. | ||
+ | {{: | ||
+ | |||
+ | ---- | ||
+ | |||
+ | **After Correction**\\ | ||
+ | {{: | ||
+ | {{: | ||
+ | |||
+ | |||
+ | ---- | ||
+ | |||
+ | ---- | ||
+ | |||
+ |
blogtng/2010-05-04/photobleaching_correction_3d_time_series.1272967709.txt.gz · Last modified: 2016/05/24 12:46 (external edit)