*** Entries to program tiltalign *** ModelFile = WTI042413_1series4.fid ImageFile = WTI042413_1series4.preali ImagesAreBinned = 1 OutputModelFile = WTI042413_1series4.3dmod OutputResidualFile = WTI042413_1series4.resid OutputFidXYZFile = WTI042413_1series4fid.xyz OutputTiltFile = WTI042413_1series4.tlt OutputXAxisTiltFile = WTI042413_1series4.xtilt OutputTransformFile = WTI042413_1series4.tltxf RotationAngle = 168.0 TiltFile = WTI042413_1series4.rawtlt AngleOffset = 0.48 BeamTiltOption = 0 RotOption = 1 RotDefaultGrouping = 5 LocalRotOption = 3 LocalRotDefaultGrouping = 6 TiltOption = 5 TiltDefaultGrouping = 5 LocalTiltOption = 5 LocalTiltDefaultGrouping = 6 MagReferenceView = 1 MagOption = 1 MagDefaultGrouping = 4 LocalMagReferenceView = 1 LocalMagOption = 3 LocalMagDefaultGrouping = 7 XStretchOption = 0 XStretchDefaultGrouping = 7 LocalXStretchOption = 0 LocalXStretchDefaultGrouping = 7 SkewOption = 0 SkewDefaultGrouping = 11 LocalSkewOption = 0 LocalSkewDefaultGrouping = 11 ResidualReportCriterion = -2.0 SurfacesToAnalyze = 2 MetroFactor = 0.25 MaximumCycles = 1000 AxisZShift = -26.6 LocalAlignments = 0 OutputLocalFile = WTI042413_1series4local.xf TargetPatchSizeXandY = 700,700 MinSizeOrOverlapXandY = 0.5,0.5 MinFidsTotalAndEachSurface = 8,3 FixXYZCoordinates = 0 LocalOutputOptions = 1,0,1 *** End of entries *** FORMATTED new file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.tlt FORMATTED new file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.xtilt FORMATTED new file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.tltxf FORMATTED ro file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.rawtlt Variable mappings View Rotation Tilt (+ incr.) Mag Comp Dmag Skew 1 rot 1 tilt 1 fixed fixed fixed fixed 2 rot 2 t 1+ 4 mag 2 fixed fixed fixed 3 rot 3 t 1+ 4 mag 3 fixed fixed fixed 4 rot 4 tilt 4 mag 4 fixed fixed fixed 5 rot 5 t 4+ 7 mag 5 fixed fixed fixed 6 rot 6 t 4+ 7 mag 6 fixed fixed fixed 7 rot 7 tilt 7 mag 7 fixed fixed fixed 8 rot 8 t 7+ 12 mag 8 fixed fixed fixed 9 rot 9 t 7+ 12 mag 9 fixed fixed fixed 10 rot 10 t 7+ 12 mag 10 fixed fixed fixed 11 rot 11 t 7+ 12 mag 11 fixed fixed fixed 12 rot 12 tilt 12 mag 12 fixed fixed fixed 13 rot 13 t 12+ 17 mag 13 fixed fixed fixed 14 rot 14 t 12+ 17 mag 14 fixed fixed fixed 15 rot 15 t 12+ 17 mag 15 fixed fixed fixed 16 rot 16 t 12+ 17 mag 16 fixed fixed fixed 17 rot 17 tilt 17 mag 17 fixed fixed fixed 18 rot 18 t 17+ 22 mag 18 fixed fixed fixed 19 rot 19 t 17+ 22 mag 19 fixed fixed fixed 20 rot 20 t 17+ 22 mag 20 fixed fixed fixed 21 rot 21 t 17+ 22 mag 21 fixed fixed fixed 22 rot 22 tilt 22 mag 22 fixed fixed fixed 23 rot 23 t 22+fix mag 23 fixed fixed fixed 24 rot 24 t 22+fix mag 24 fixed fixed fixed 25 rot 25 t 22+fix mag 25 fixed fixed fixed 26 rot 26 t 22+fix mag 26 fixed fixed fixed 27 rot 27 t 22+fix mag 27 fixed fixed fixed 28 rot 28 fixed mag 28 fixed fixed fixed 29 rot 29 t 34+fix mag 29 fixed fixed fixed 30 rot 30 t 34+fix mag 30 fixed fixed fixed 31 rot 31 t 34+fix mag 31 fixed fixed fixed 32 rot 32 t 34+fix mag 32 fixed fixed fixed 33 rot 33 t 34+fix mag 33 fixed fixed fixed 34 rot 34 tilt 34 mag 34 fixed fixed fixed 35 rot 35 t 34+ 40 mag 35 fixed fixed fixed 36 rot 36 t 34+ 40 mag 36 fixed fixed fixed 37 rot 37 t 34+ 40 mag 37 fixed fixed fixed 38 rot 38 t 34+ 40 mag 38 fixed fixed fixed 39 rot 39 t 34+ 40 mag 39 fixed fixed fixed 40 rot 40 tilt 40 mag 40 fixed fixed fixed 41 rot 41 t 40+ 45 mag 41 fixed fixed fixed 42 rot 42 t 40+ 45 mag 42 fixed fixed fixed 43 rot 43 t 40+ 45 mag 43 fixed fixed fixed 44 rot 44 t 40+ 45 mag 44 fixed fixed fixed 45 rot 45 tilt 45 mag 45 fixed fixed fixed 46 rot 46 t 45+ 50 mag 46 fixed fixed fixed 47 rot 47 t 45+ 50 mag 47 fixed fixed fixed 48 rot 48 t 45+ 50 mag 48 fixed fixed fixed 49 rot 49 t 45+ 50 mag 49 fixed fixed fixed 50 rot 50 tilt 50 mag 50 fixed fixed fixed 51 rot 51 t 50+ 55 mag 51 fixed fixed fixed 52 rot 52 t 50+ 55 mag 52 fixed fixed fixed 53 rot 53 t 50+ 55 mag 53 fixed fixed fixed 54 rot 54 t 50+ 55 mag 54 fixed fixed fixed 55 rot 55 tilt 55 mag 55 fixed fixed fixed 56 rot 56 t 55+ 58 mag 56 fixed fixed fixed 57 rot 57 t 55+ 58 mag 57 fixed fixed fixed 58 rot 58 tilt 58 mag 58 fixed fixed fixed 59 rot 59 t 58+ 61 mag 59 fixed fixed fixed 60 rot 60 t 58+ 61 mag 60 fixed fixed fixed 61 rot 61 tilt 61 mag 61 fixed fixed fixed Variable Metric minimization Initial F: 6.432652 Cycle 10 2.116755 Cycle 20 1.099803 Cycle 30 0.842558 Cycle 40 0.771461 Cycle 50 0.760875 Cycle 60 0.759789 Cycle 70 0.759682 Number of cycles : 70 Final F : 0.759682 61 views, 134 geometric variables, 21 3-D points, 1281 projection points Ratio of total measured values to all unknowns = 2562/ 314 = 8.16 At minimum tilt, rotation angle is 169.98 view rotation tilt deltilt mag dmag skew mean resid 1 171.6 61.1 0.63 1.0000 0.0000 0.00 1.07 2 171.5 59.1 0.58 0.9989 0.0000 0.00 0.97 3 171.4 57.0 0.53 0.9997 0.0000 0.00 0.88 4 171.3 55.0 0.48 0.9992 0.0000 0.00 0.88 5 171.2 53.0 0.52 0.9999 0.0000 0.00 0.93 6 171.1 51.0 0.55 0.9997 0.0000 0.00 0.92 7 171.0 49.1 0.58 0.9999 0.0000 0.00 0.79 8 171.0 47.0 0.55 0.9996 0.0000 0.00 0.74 9 170.9 45.0 0.52 0.9996 0.0000 0.00 0.70 10 170.8 43.0 0.49 0.9993 0.0000 0.00 0.66 11 170.8 40.9 0.46 0.9994 0.0000 0.00 0.60 12 170.7 38.9 0.42 0.9995 0.0000 0.00 0.68 13 170.7 36.9 0.39 0.9999 0.0000 0.00 0.61 14 170.6 34.8 0.36 0.9993 0.0000 0.00 0.45 15 170.5 32.8 0.32 0.9991 0.0000 0.00 0.57 16 170.5 30.8 0.29 0.9991 0.0000 0.00 0.51 17 170.4 28.7 0.25 0.9993 0.0000 0.00 0.64 18 170.4 26.7 0.25 0.9993 0.0000 0.00 0.43 19 170.4 24.7 0.25 0.9988 0.0000 0.00 0.47 20 170.3 22.7 0.24 0.9991 0.0000 0.00 0.53 21 170.3 20.7 0.24 0.9987 0.0000 0.00 0.64 22 170.2 18.7 0.24 0.9986 0.0000 0.00 0.63 23 170.2 16.7 0.20 0.9982 0.0000 0.00 0.48 24 170.2 14.6 0.16 0.9988 0.0000 0.00 0.48 25 170.1 12.6 0.12 0.9983 0.0000 0.00 0.56 26 170.1 10.6 0.08 0.9985 0.0000 0.00 0.55 27 170.1 8.5 0.04 0.9985 0.0000 0.00 0.54 28 170.0 6.5 0.00 0.9984 0.0000 0.00 0.72 29 170.0 4.6 0.10 0.9985 0.0000 0.00 0.75 30 170.0 2.7 0.20 0.9982 0.0000 0.00 0.61 31 170.0 0.8 0.30 0.9985 0.0000 0.00 0.45 32 170.0 -1.1 0.40 0.9982 0.0000 0.00 0.51 33 170.0 -3.0 0.50 0.9984 0.0000 0.00 0.45 34 170.0 -4.9 0.61 0.9987 0.0000 0.00 0.70 35 170.0 -6.9 0.60 0.9986 0.0000 0.00 0.70 36 169.9 -8.9 0.60 0.9989 0.0000 0.00 0.76 37 169.9 -10.9 0.60 0.9989 0.0000 0.00 0.61 38 169.9 -12.9 0.59 0.9988 0.0000 0.00 0.62 39 170.0 -14.9 0.59 0.9988 0.0000 0.00 0.55 40 169.9 -16.9 0.59 0.9989 0.0000 0.00 0.41 41 170.0 -18.9 0.59 0.9986 0.0000 0.00 0.50 42 169.9 -20.9 0.59 0.9994 0.0000 0.00 0.46 43 170.0 -22.9 0.59 0.9990 0.0000 0.00 0.49 44 170.0 -24.9 0.58 0.9989 0.0000 0.00 0.45 45 170.0 -26.9 0.58 0.9991 0.0000 0.00 0.49 46 170.0 -28.9 0.59 0.9994 0.0000 0.00 0.54 47 170.0 -30.9 0.60 0.9990 0.0000 0.00 0.49 48 170.0 -32.9 0.61 0.9995 0.0000 0.00 0.62 49 170.0 -34.9 0.62 0.9991 0.0000 0.00 0.66 50 170.1 -36.9 0.63 0.9991 0.0000 0.00 0.60 51 170.1 -38.9 0.63 0.9990 0.0000 0.00 0.50 52 170.1 -40.9 0.62 0.9994 0.0000 0.00 0.62 53 170.1 -42.9 0.61 0.9993 0.0000 0.00 0.77 54 170.1 -44.9 0.60 0.9993 0.0000 0.00 0.73 55 170.2 -46.9 0.59 0.9992 0.0000 0.00 0.80 56 170.2 -48.9 0.60 0.9992 0.0000 0.00 0.74 57 170.3 -50.9 0.60 0.9994 0.0000 0.00 0.77 58 170.3 -52.9 0.61 0.9997 0.0000 0.00 0.88 59 170.4 -54.9 0.60 0.9999 0.0000 0.00 0.99 60 170.4 -56.9 0.58 0.9996 0.0000 0.00 0.83 61 170.4 -58.9 0.57 0.9998 0.0000 0.00 0.96 3-D point coordinates (with centroid zero) # X Y Z obj cont mean resid 1 220.19 177.84 -133.14 1 1 0.79 2 50.72 76.54 44.26 1 2 0.63 3 -20.58 -207.47 42.77 1 3 0.60 4 -21.42 -83.49 53.68 1 4 0.60 5 -95.26 -102.14 30.41 1 5 0.55 6 -0.59 -434.71 40.66 1 6 0.72 7 75.13 -488.55 33.39 1 7 0.61 8 113.71 -329.90 52.79 1 8 0.65 9 129.97 -767.95 47.78 1 9 0.56 10 -7.71 -604.48 -30.11 1 10 0.75 11 -105.02 -420.31 19.81 1 11 0.44 12 233.57 529.64 47.95 1 12 0.90 13 -227.33 181.79 26.09 1 13 0.64 14 -169.51 398.14 35.04 1 14 0.44 15 -210.87 449.11 -82.94 1 15 0.79 16 -115.55 520.33 -103.98 1 16 0.64 17 -216.45 645.10 38.92 1 17 0.59 18 -206.72 729.98 36.95 1 18 0.65 19 35.25 732.95 -124.32 1 19 0.74 20 480.19 -323.51 -109.22 1 20 0.83 21 58.27 -678.90 33.21 1 21 0.53 Midpoint of Z range relative to centroid in Z: -39.73 FORMATTED new file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.resid Residual error mean and sd: 0.649 0.395 Projection points with large residuals obj cont view index coordinates residuals # of # # # X Y X Y S.D. 1 12 11 683.55 390.03 -0.11 -2.07 3.59 1 12 13 677.67 390.69 -0.31 -1.67 3.52 1 12 34 678.40 390.20 0.88 1.62 3.34 1 12 6 706.79 385.73 -1.61 -1.59 3.21 1 20 41 569.03 1275.13 0.67 1.02 3.20 1 12 9 691.30 388.43 -1.34 -1.50 3.11 1 1 59 700.64 749.40 0.69 -2.35 2.99 1 20 61 674.15 1263.74 -0.04 -2.67 2.99 1 1 55 700.86 747.56 -0.33 -1.81 2.76 1 19 29 842.02 154.99 1.05 1.43 2.73 1 8 16 910.74 1222.52 0.33 -1.36 2.68 1 15 50 1025.29 414.52 -0.46 -1.20 2.67 1 10 8 1091.06 1469.43 -0.13 1.84 2.65 1 20 2 864.73 1220.50 -0.48 2.34 2.65 1 19 59 722.35 181.56 -2.13 -0.72 2.60 1 19 36 813.92 160.21 1.33 1.02 2.51 1 12 5 710.20 385.48 -0.53 -1.91 2.49 1 15 12 1113.65 397.99 1.02 1.21 2.48 1 8 21 918.47 1218.65 0.71 1.28 2.45 1 20 59 655.74 1264.46 1.59 -1.45 2.42 1 12 45 716.91 384.05 -0.32 1.09 2.41 1 16 46 951.26 354.24 -0.57 -1.01 2.35 1 1 1 952.28 701.63 0.63 2.14 2.35 1 12 39 693.15 387.94 0.82 0.94 2.32 1 15 17 1126.79 394.86 1.07 0.61 2.29 1 12 1 738.54 382.08 -0.39 -2.15 2.27 1 1 61 703.66 749.96 -0.89 -2.07 2.27 1 18 61 973.89 143.22 -2.16 -0.54 2.23 1 16 39 988.90 347.38 -0.03 -1.21 2.20 1 8 26 930.20 1217.24 -0.55 0.98 2.19 1 10 4 1088.47 1471.13 -0.76 1.65 2.17 1 2 24 918.57 809.37 -0.87 -0.60 2.17 1 4 29 1027.11 952.46 -1.47 -0.45 2.14 1 15 10 1108.28 399.70 -0.24 1.58 2.14 1 20 32 577.75 1273.28 0.29 0.90 2.07 1 19 48 765.08 169.09 0.58 1.04 2.07 1 12 47 724.50 382.92 0.83 0.81 2.06 1 16 36 1001.74 345.24 0.24 -1.48 2.05 FORMATTED new file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4fid.xyz SURFACE ANALYSIS: The following parameters are appropriate if fiducials are all on one surface Fit of one plane to all fiducials: Adjusted slope = -0.1656 Incremental tilt angle change = 9.40 Total tilt angle change = 9.88 The following parameters are provided to indicate the consistency of the fit when fiducials are on two surfaces Fit of one plane to points on bottom surface: # of points = 7 Z axis intercept = -59.26 Adjusted slope = -0.1856 Mean residual = 23.239 X axis tilt needed = 5.54 Incremental tilt angle change = 10.51 Total tilt angle change = 10.99 Fit of one plane to points on top surface: # of points = 14 Z axis intercept = 41.05 Adjusted slope = 0.0496 Mean residual = 5.804 X axis tilt needed = -0.42 Incremental tilt angle change = -2.84 Total tilt angle change = -2.36 The following parameters combine the last two results and are appropriate if fiducials are on two surfaces Thickness at Z intercepts = 100.31 Average adjusted slope = -0.0288 Average X axis tilt needed = 1.57 Incremental tilt angle change = 1.65 Total tilt angle change = 2.13 Unbinned thickness needed to contain centers of all fiducials = 145. Incremental unbinned shift needed to center range of fiducials in Z = 9.2 Total unbinned shift needed to center range of fiducials in Z = -17.4 *** Entries to program xfproduct *** InputFile1 = WTI042413_1series4.prexg InputFile2 = WTI042413_1series4.tltxf OutputFile = WTI042413_1series4_fid.xf *** End of entries *** FORMATTED ro file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.prexg FORMATTED ro file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.tltxf 61 transforms in first file 61 transforms in second file FORMATTED new file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4_fid.xf 61 new transforms written SUCCESSFULLY COMPLETED