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===Decoding PGP1F with Agi26k0gap Padlock Probe – 2nd full decoding=== ====Sample==== *This PGP1F MatTek dish was **S2, 1st rolonies made at 2014-04-10 **2nd rolonies finished at 2014-04-14 **2 color dye + 5 cycle decoding done at 2014-04-14 *Matt run 7 cycle decoding - 2014-08-28 *Data stored 2014-08-28 folder ====Procedure==== *#Align all images based on BF *#Shift and crop images of every steps, make MIP image with all steps of aligned and cropped images *#Count 1st Rolony by PISA *#Count 1st Rolony and make BW image from MIP of all step images by PISA *#*PISA param test and apply *#*PISA parameter *#*PISAParam.log_radius = 3; *#*PISAParam.log_upper = -2e-4; *#*PISAParam.area_upper = 100; *#*PISAParam.area_lower = 10; *#*PISAParam.axratio_lower = 0.5; *#*PISAParam.circ_upper = 1.6; *#*PISAParam.circ_lower = 0.8; *#*PISAParam.pconn = 8; *#*PISAParam.bkgmult_lower = 3; *#*PISAParam.FilterOption = 1; *#*PISAParam.Deconvoluted = 0; *#*PISAParam.DoMedflt = 1; *#*PISAParam.nofindbkg = 0; *#Run Script (will be specified later...) ====Result==== *Result *Number of cells : Pos1 ~ 120, Pos2 : 100 *1st Rolony : **Pos1 : 31371, 261.43/cell **Pos2 : 27354, 273.54/cell *MIP of all steps : *Pos1 : 6621, 55.18/cell *Pos2 : 4739, 47.39/cell *Even if 2nd full decoding sample has more 1st rolonies, it has less number of decoded features… *To DO : Decode this with 63x!!!, and compare RNA expression data from Jay’s or Zhang Lab’s =====Comparison of 1st rolonies between 1st decoding and 2nd decoding===== *[[File:1stRolonyFigure_Count_Plot_Pos1_2014-08-29.png|1200px]] =====Decoded counts and gene mapping table : position 1===== *[[File:DecodeResult_Count_Plot_Pos1_2014-08-29.png|700px]] [[File:DecodeResult_MarkBarcode_Pos1_2014-08-29.png|800px]] =====Decoded counts and gene mapping table : position 2===== *[[File:DecodeResult_Count_Plot_Pos2_2014-08-29.png|700px]] [[File:DecodeResult_MarkBarcode_Pos2_2014-08-29.png|800px]] =====Comparison of color distribution between 1st decoding and 2nd decoding(position 1)===== *[[File:DecodeResult_Count_Plot_Compare_2014-08-29.png|600px]]
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