Hosuk:LabNotes/2013-12-11

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Revision as of 03:56, 12 December 2013 by >Hosuki78 (→‎Result(Preliminary))
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NCIH1975 Rolony : 2nd sample

  • Sample : Glass-bottom MatTek dish – 1 dishes
  • NCIH1975 P27 (from Illumina)
  • Process 12/09 ~ 12/11
  • Image Cy5-1st Rolony detection probe (1uM in 30% Formamide + 2xSSC)

Image condition

  • Laser = 2%
  • PMT Gain = 550
  • Z stack = 0.25um step, 199 images
    • allows higher resolution along Z axis, and better 3D view


Result

  • This cells were more denser than previous sample.
  • The number of rolonies were many.
  • PISA counting = 14557
    • PISA Param
      • Gaussian std = 3, upper = -3e-4
      • area upper = 100, lower = 2, axratio lower = 0.7
      • circ upper = 1.6, lower = 0.8, perim conn = 8
      • bkgmult lower = 7

3D view with ImageJ

  • Procedure : Stack all images --> Crop (because ImageJ can’t handle a big size) --> Run 3D plugin

File:MAX Fullsize Cropped Stack NCIH1975-20131211 Step3 Pos1.png


File:3DView MAX Cropped Stack NCIH1975-20131211 Step3 Pos1.png