run("bin image jru v1", "bin_type=[Spatial Bin] cumulative? bin_by_x?=4 bin_by_y?=2"); run("bin image jru v1", "bin_type=[Spatial Bin] cumulative? bin_by_x?=1 bin_by_y?=20"); rename("overview"); waitForUser("Select Line (width is typically 4)"); //the time per line here assumes 15.3 ms lines or 6.39 us pixel dwell time on zeiss systems (2x temporal bin multiplies the line time by 2) run("get line traj jru v1", "binned_image=overview original_image=[Binned Stack] time_per_line(ms)=30.5"); run("export plot jru v1"); //this version gives manual fitting //run("analysis cross corr v2", "sampling=20000 psf=2Dxz_Gaussian file=[PlotWindow trajectory] show traj=20 segmented detrending=3"); //here is the version for automated fitting run("analysis cross corr v2", "sampling=20000 psf=2Dxz_Gaussian file=[PlotWindow trajectory] show traj=20 segmented detrending=3 simple min_green=5 max_green=1000 min_red=5 max_red=1000 min_cc=5 max_cc=1000 cc_taud_fitting=Avg_green_red"); run("export plot jru v1"); //run("close");