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 10:18] – 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 basically be used for intensity quantification (FRAP, on the other hands, correct bleaching after measuring the raw image). If you are analyzing shapes or positions, no problem for quantification. | + | By the way, bleaching corrected images cannot basically be used for intensity quantification (FRAP, on the other hands, correct bleaching after measuring the raw image). If you are analyzing shapes or positions, no problem for quantification. |
+ | |||
+ | ---- | ||
+ | |||
+ | 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.1272968288.txt.gz · Last modified: 2016/05/24 12:46 (external edit)