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==Stitching Results Into Tile== *DecodePxPx.m results containing coordinate info is stored in StatTable matrix saved in 'Analysis_BA8_suppv2_2015-10-29_PosX_Try_1.mat' **Column order: Index, Area, Avg Intensity, X Coordinate, Y Coordinate, Total Count *Output following info into one consolidated excel file: **Column order: GeneName, GeneBarcode, Area, X Coordinate, Y Coordinate **Use script RolonyPositionExcels.m *Aligned/Cropped image sizes **Pos1: 2044 **Pos2: 2046 **Pos3: 2046 **Pos4: 2044 **Pos5: 2044 **Pos6: 2046 **Pos7: 2046 **Pos8: 2046 **Pos9: 2046 *Finding size of overlap between each position **Based on stage coordinates expect overlap size to be 295px = 84um **To find actual overlap compare positions of decoded rolonies ***Did this manually so only looked at most abundant gene 'SNAP25' ***In the same region, more rolonies decoded at the bottom of previous image then top of latter image ****E.g. More SNAP25 in bottom 279px of Pos1 than in top 279px of Pos2 ****Could be due to photobleaching? "uneven illumination" or equivalent phenomena for confocal? *Offsets (calculated average Y-offset of SNAP25 rolonies that overlapped) **Pos1->2: 279 **Pos2->3: 289 **Pos3->4: 298 **Pos4->5: 278 **Pos5->6: 278 **Pos6->7: 305 **Pos7->8: 280 **Pos8->9: 299 *Stitched Tile A: **Use count of previous position for overlapping region *Stitched Tile B: **Use count of latter position for overlapping region
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