Hosuk:LabNotes/2013-12-15
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Rolony Counting in 3D[edit]
- First of all, run PISA with all individual stacks,
- Record all information about each Rolony – stack, center position, average area, average intensity
- Look from the first stack, which is the very bottom image, (the lowest z position)
- Check the rolonies across all stacks with center position (x, y cordinate)
- Finally select Rolonies which present at least 2 stacks.
Result[edit]
- 2D Maxim projection image : # = 1040
- 3D 199 stacks, count with 3D space : # = 1852
Parameters[edit]
- Data : NCIH1975, generated at 2013-12-11
- Size after cropped : 513 x 513
- 0.25um delta Z, 199 Stacks, Crop_NCIH1975-20131211_Step3_Pos1_z000 ~ z198
- Z size filtering : select Rolony which present at least 2 stacks (~about above 0.5um)
- PISA parameter
- PISAParam.log_radius = 3;
- PISAParam.log_upper = -2e-4;
- PISAParam.area_upper = 50;
- PISAParam.area_lower = 4;
- PISAParam.axratio_lower = 0.6;
- PISAParam.pconn = 8;
- PISAParam.circ_upper = 1.6;
- PISAParam.circ_lower = 0.8;
- PISAParam.bkgmult_lower = 7;
Figures[edit]
- Matlab plot figure file : Plot
File:Snapshot ImageJ Matlab 3D Crop NCIH1975-20131211 Step3 Pos1.png
Result with 2048 x 2048 image[edit]
- 2D Maxim projection image : # = 14457 (LabNote 2013-12-11)
- 3D 199 stacks, count with 3D space : # = 30603
(Process time : 971.37sec = 16.1 min)