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)