Hosuk:LabNotes/2014-8-22

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Decoding with Agi26k0gap Padlock Probe : Masking images with MIP of all steps[edit]

Masking[edit]

  • Done by Matt
  • MIP with images of all steps
  • Run PISA of the MIP
    • seg_data = regionprops(MaskedFile,MaskedImgFile, 'MeanIntensity', 'Area', 'Centroid');



Variables[edit]

  • After masking
    • DecodeInfoMaxNum : Total number of features by regionprops
    • DecodeInfo_MeanIntensity(1:MaxRolonyNum, 1:NumOfSteps) : Mean intensity of each feature
    • RolonyInfo_Area(1:MaxRolonyNum, 1): Area(number of pixels) of each feature
    • RolonyInfo_CenterY(1:MaxRolonyNum, 1) : Centroid X of each feature
    • RolonyInfo_CenterX(1:MaxRolonyNum, 1): Centroid Y of each feature


  • After normalize
    • Max_MeanIntensity(1:MaxRolonyNum, 1) : Max intensity of each Step1 ~ Step21
    • DecodeInfo_NormMeanIntensity(1:MaxRolonyNum, 1:NumOfSteps) : Normalized by Max
      • DecodeInfo_NormMeanIntensity = DecodeInfo_MeanIntensity / Max_MeanIntensity;
    • DecodeInfo_Sqrt(1:DecodeInfoMaxNum, 1:NumOfDecodingSlots) : sqrt of sum of sq of each intensity = sqrt[ (I_488)^2 + (I_Cy3)^2 + (I_Cy5)^2 ]
    • DecodeInfo_NormMeanIntensity2(1:MaxRolonyNum, 1:NumOfSteps) : norm intensity after filtered out the weak signal
      • all intensity = 0 when DecodeInfo_Sqrt < thresh_val (it is 0.1 for now)
    • DecodeInfo_NormMeanIntensity_Result(1:MaxRolonyNum, 1:NumOfSteps) : normalized again by norm_tetra_3, plot cloud with this
      • [DecodeInfo_NormMeanIntensity_Result, cms, calls, coords_3d] = norm_tetra_3(DecodeInfo_NormMeanIntensity2, NumOfSteps, thresh_subvalue);



Normalized intensity distribution[edit]

  • all intensity = 0 when DecodeInfo_Sqrt < thresh_val
  • Blue : 488, Green : Cy3, Red : Cy5

File:DecodeResult CloudPlots 2014-08-21.png


Result[edit]

File:DecodeResultSummary 1 2014-08-21.png


File:DecodeResult MappedfeatureTo1stROolony 2014-08-21.png File:DecodeResult MappedfeatureToBF 2014-08-21.png