solvematch(1) General Commands Manual solvematch(1)NAMEsolvematch - Solve for transformation matching one tomogram to anotherSYNOPSISsolvematch [options]DESCRIPTIONSolvematch will solve for a 3-dimensional linear transformation relat- ing the tomogram volumes resulting from tilt series around two differ- ent axes. It can use information from the 3-D coordinates of fiducials found by Tiltalign, or from IMOD models of corresponding points in the two volumes, or from both of these sources together. Current ver- sions of Tiltalign produce fiducial lists with coordinates correspond- ing the coordinates in the tomogram, thus providing all of the informa- tion that Solvematch needs to find the transformation. Older versions of Tiltalign produced coordinates centered around zero; this situa- tion is discussed below.UsingFiducialCoordinatesWhen you use fiducial coordinates, the program needs to know how the fiducial points correspond between the two tilt series. There are two different ways that this information can be provided. If Transferfid was used to produce the seed model for one of the axes from the fiducial model for the other, then it can be given an option to produce a file with the coordinates of corresponding fiducial points from one view in each data set. This file can be provided to Solvematch with the "-transfer" option and the program will be able to deduce how the points in the fiducial lists from Tiltalign corre- spond. This capability allows you to add or delete fiducial points in either fiducial model after running Transferfid without having to keep track of how this affects the correspondence between points. This option requires that both fiducial models be supplied to Solvematch. Also, it is essential that Solvematch be informed if the A axis is being matched to the B axis, with the -atob option. In the absence of a transfer coordinate file, the program needs lists of points that correspond between the two data sets. If it is given a small list of points which do correspond, it can find the rest of the correspondences and ignore any points from either set that do not have a mate. There are two restrictions in using this capability. First, one must identify at least 4 initial correspondences; in fact, having at least 5 is recommended. Second, if there are fiducials on both sur- faces of the section, this initial list must include at least one from each surface. When you enter point numbers, use the numbers listed on the left in the fiducial coordinate file. These numbers may not correspond to the con- tour numbers in the original fiducial model if some contours were not included in the solution. These numbers do not need to be sequential; i.e., you can delete points from the coordinate file. The program will refer to points by these numbers. When you have both fiducial coordi- nates and points from matching models, it will refer to the latter points by the negative of their point number. When using fiducial coordinates, you also need to indicate to Solve- match whether the gold fiducials are on one surface or distributed in depth (typically but not necessarily on two surfaces). If there is gold on only one surface, you must determine whether the two tomograms are inverted in Y (Z in flipped orientation); i.e. whether the gold is on the "top" of the section in one tomogram and the "bottom" in the other even though they can be superimposed by a rotation. The program needs to know this because there is no reliable information about this polarity in the fiducial coordinates. However, such an inversion should be impossible when data are acquired with a CCD camera.UsingMatchingModelsWhen fiducial points from Tiltalign are not available, the best option for dual-axis tomograms is to use Dualvolmatch instead of Solvematch. Otherwise, you can use models of corresponding points to register the two volumes in Solvematch. Pick a set of points that can be localized well in both tomograms and enter them in the same order into a model for each tomogram. The points can be in the same or in different objects or contours, as long as they occur in the same order in each model. The points should be well-distributed in all dimen- sions, and they must not all be in one plane. At least 8 points are recommended. If this is to provide the basis for the final alignment of the volumes, they should be relatively near the 8 corners of the volume, and more points should be used for greater accuracy; but if the alignment is to be refined with correlation, this is not necessary.UsingOld,RelativeFiducialCoordinatesWith fiducial coordinates from older versions of Tiltalign, the pro- gram can solve for the 3 by 3 transformation but not for the shifts in X, Y and Z. There are several ways to get these shifts: by rerunning Tiltalign to get absolute coordinates; by finding the transformation with Dualvolmatch, or by giving Solvematch models of corresponding points in the two tomograms. If you create matching models, 3-6 points are recommended. If fiducials are essentially on one surface, then the modeled points are needed to find the scaling in Y (Z in flipped orien- tation) between the two tomograms. In this case, be sure to distribute the points in depth (rather than all on one surface) and use 5-6 points so as to provide information on this scaling.LocalFittingSometimes the fit to the fiducial points gives a high maximum residual error because there is a big nonlinear distortion between the two vol- umes. In these cases, fitting to local sets of points can be used to determine that the fiducials have been properly identified and that the global fit is as good as it is ever going to be. If the LocalFitting option is selected, the program will try local fits when the maximum residual is above the specified limit. It determines the size of the area that, on average, would contain the specified minimum number of points. It then sets up local areas of this size, overlapping by 50%, and expands an area if necessary to contain the minimum number of points. It performs fits to the points in each area and reports the results of the fits. If the overall maximum residual is less than 1.5 times the specified limit, and no more than 5% of the areas have maxi- mum residuals above this limit, the fit is considered adequate. If local fitting is being done, then the program will also compute a local fit to points at the center of the volume so as to determine how far the global 3D transformation will shift data at the center of the volume out of alignment. If this shift is large enough, then corrsearch3d may have trouble starting to find the alignment of the data. Thus, if the program finds that this shift is bigger than a specified limit, it recommends initial shifts to be used when running corrsearch3d and may also recommend that the initial matching volume be made the same size as the volume being transformed. It will exit with an error so that you can adjust these parameters before proceed- ing.ProgramOperationThe program will automatically remove "outliers", pairs of points that are likely to be incorrect because their residual errors are so extreme relative to the other points. Up to 10% of points may be removed in this way. If, even after removing such outliers, the maximum residual in the linear fit is still higher than a value that you specify, then the program will exit with an error. The program determines the transformation and computes the deviation between each actual point in the first tomogram and the transformation of the corresponding point in the second tomogram. It reports the mean and S.D. of these deviations, the number of the point with the highest deviation, and the magnitude of its deviation.OPTIONSSolvematch uses the PIP package for input (see the manual page for pip) and can also take input interactively to maintain compatibility with old command files. The following options can be specified either as command line arguments (with the -) or one per line in a command file or parameter file (without the -). Options can be abbreviated to unique letters; the currently valid abbreviations for short names are shown in parentheses.-output(-o)OR-OutputFileFilenameOutput file for 3D transformation. This entry may be omitted.-afiducials(-af)OR-AFiducialFileFilenameName of file with coordinates of fiducials from the first tilt series. To solve for the transformation using matching models only, omit this entry.-bfiducials(-bf)OR-BFiducialFileFilenameName of file with coordinates of fiducials from the second tilt series. This entry is not needed when using matching models only.-alist(-al)OR-ACorrespondenceListListofintegerrangesA list of the points in series 1 for which a corresponding point in series 2 is known with confidence. Ranges may be entered (e.g. 1-5,7,6,12). This entry and the following one are not needed when a coordinate file from transferfid is available. The default is that all points correspond between the two series.-blist(-bl)OR-BCorrespondenceListListofintegerrangesA list of the corresponding points in the second series. The same number of values must be entered in this list as in the preceding list. Again, the default is that all points corre- spond between the two series.-transfer(-t)OR-TransferCoordinateFileFilenameFile of matching fiducial coordinates produced by running trans- ferfid with the -c option.-amodel(-amo)OR-AFiducialModelFilenameName of fiducial model file for first tilt series. This entry is needed only when a transfer coordinate file is being used.-bmodel(-bmo)OR-BFiducialModelFilenameName of fiducial model file for second tilt series. This entry is needed only when a transfer coordinate file is being used.-useOR-UsePointsListofintegerrangesList of starting points to use from the A axis (the first series taken). The program will start with these correspondences and add other pairs of points that appear to correspond.-atobOR-MatchingAtoBThe first series here (referred to as A in these options) is the B axis, i.e. the second tilt series taken, and the second series is the A axis.-xtilts(-x)OR-XAxisTiltsTwofloatsThe values of X axis tilt that were used in generating the first and second tomograms. These angles are needed to make the fidu- cial coordinates from Tiltalign correspond to the actual posi- tions of the particles in the tomograms. The default values are 0.-angles(-ang)OR-AngleOffsetsToTiltTwofloatsThe values of tilt angle offsets that were used when running Tilt to generate the first and second tomograms. These are dif- ferent from the angle offsets used when running Tiltalign, which need not be supplied to Solvematch. The default values are 0.-zshifts(-z)OR-ZShiftsToTiltTwofloatsThe values of Z shift that were used when running Tilt to gener- ate the first and second tomograms. These are different from the Z shifts used when running Tiltalign, which need not be sup- plied to Solvematch. The default values are 0.-surfaces(-su)OR-SurfacesOrUseModelsIntegerThis entry governs the mode of operation of the program. To obtain the transformation from fiducial points only, enter: 2 if there are fiducials on two surfaces, 1 or -1 if fiducials are on only one surface, 0 to use model files of corresponding points; with this entry both the matching model points and fiducial points will be used if the fiducials are available. -2 to use only the matching model points and ignore any entries of fiducial point files. The default is 2. When 1 or -1 is entered, the program will determine whether the tomograms are upside-down from each other (i.e., inverted in depth) by assuming that the tomograms have the same handedness.-inverted(-i)OR-InvertedInDepthIntegerThis option can be used with a-surfacesentry of 1 to prevent the program from analyzing whether tomograms are inverted by assuming that they have the same handedness. Enter 1 if tomo- grams are inverted in the depth dimension, or 0 if they are not. Tomograms are inverted if features at high Z in one tomogram are at low Z in the other; this property is independent of whether they are mirror images of each other. This entry should be needed only if tomograms are in fact mirror images.-maxresid(-m)OR-MaximumResidualFloatingpointThe limiting value for the maximum residual, so that the program will exit with an error if this value is exceeded.-local(-l)OR-LocalFittingIntegerMinimum number of points required in each local area if local fitting is desired. The default is 0, which disables local fits. Non-zero values must be at least 6.-center(-c)OR-CenterShiftLimitFloatingpointMaximum shift between central local fit and global fit. This shift is computed and tested against this limit only when local fitting occurs, namely when the -local option is selected and the global maximum residual is greater than the -maxresid entry. If the shift is greater than the limit, the program will exit with an error, but if the solution is adequate there is no need to rerun the program. The default value is 10. A value of 0 disables the test.-amatch(-ama)OR-AMatchingModelFilenameName of model of points from the first tomogram-bmatch(-bma)OR-BMatchingModelFilenameName of model of corresponding points from the second tomogram-atomogram(-atom)OR-ATomogramOrSizeXYZTextstringEither the file name or the X, Y and Z dimensions of the first tomogram.-btomogram(-bt)OR-BTomogramOrSizeXYZTextstringEither the file name or the X, Y and Z dimensions of the second tomogram.-scales(-sc)OR-ScaleFactorsTwofloatsAmounts by which the fiducial coordinates need to be scaled to match the coordinates of the first and second tomograms, respec- tively. Each factor should be the binning of the images on which the fiducials were modeled divided by the binning of the aligned stack. The entry should not be needed in ordinary cir- cumstances. It overrides the scaling that is computed from a pixel size in the fiducial file and the pixel spacing from the tomogram header. The entry can be used as a substitute for pro- viding the image file name in the -atomogram and -btomogram options.-aniso(-ani)OR-AnisotropicLimitFloatingpointThe maximum percentage difference between the scaling along the three axes; a percentage difference greater than this limit will cause a warning to be issued. If the difference is in the Y direction and points were specified as being on two surfaces, the program will also advise that it be run with "-surfaces 1" instead. Enter 0 to disable these warnings. The default is 10%.-param(-p)OR-ParameterFileParameterfileRead parameter entries as keyword-value pairs from a parameter file.-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard input.INTERACTIVEINPUTIf the program is started with no command line arguments, it reverts to interactive input and is restricted to older modes of operation. The input takes different forms depending on what data are available. The inputs to the program when fiducials from Tiltalign are available are: Name of file with coordinates of fiducials from the first tilt series Name of file with coordinates of fiducials from the second series A list of the points in series 1 for which a corresponding point in series 2 is known with confidence, or / if all points correspond between the two series. A list of the corresponding points in the second series, or / if all points correspond between the two series. The values of X axis tilt that were used in generating the first and second tomograms. The limiting value for the maximum residual, so that the program will exit with an error if this value is exceeded. Enter either 0 to determine shifts from model files of corresponding points, or -1, 1, or 2 to determine just the 3 by 3 transformation and not the shifts. Enter 2 if there are fiducials on two surfaces, 1 if fiducials are on one surface and the tomograms are NOT inverted relative to each other, or -1 if the tomograms are inverted and there are fiducials on only one surface. IF you entered 0, make the following four entries: Either the file name or the X, Y and Z dimensions of the first tomogram Name of model of points from the first tomogram Either the file name or the X, Y and Z dimensions of the second tomogram Name of model of points from the second tomogram Finally, enter name of file for output of the transformation, or Return for none Inputs to the program when matching models alone are being used: A blank line (Return) in place of the name of the first fiducial file The limiting value for the maximum residual Either the file name or the X, Y and Z size of the first tomogram Name of model of points from the first tomogram Either the file name or the X, Y and Z size of the second tomogram Name of model of points from the second tomogram Name of file for output of the transformation, or Return for noneHISTORYWritten by David Mastronarde, 1995; modified for zero shifts, 7/4/97 Added outlier elimination and error exit, 6/5/99 Added ability to start with small initial set of matches, 3/20/00 Added ability to use matching models only, 7/21/02 Fixed treatment of single-surface case and converted to PIP, 12/24/03 Added ability to deal with absolute fiducial coordinates, 6/9/04BUGSEmail bug reports to mast at colorado dot edu. IMOD 4.10.12 solvematch(1)