4.8.6 Fitpatches
The Fitpatches tool assesses the quality of the patch displacements, and creates a set of
vector models that allow the user to manually correct aberrant vectors. Details about
this program can be found at http://bio3d.colorado.edu/imod/doc/man/fitpatches.html.
The program creates a number of vector models that can be opened and aberrant
vectors or ones with large residual values can be deleted. A description of the editing
process can be found in Sect. 12.5 of the IMOD Tomography Guide (http://bio3d.
colorado.edu/imod/doc/tomoguide.html). If models are edited, Fitpatches is run again
to convert the corrected vector models back into text files with displacements.
4.8.7 Stitchalign
The Stitchalign tool takes the edge vectors from Edgepatches or Fitpatches and
calculates two components needed for the final alignment. One is a set of linear
transforms appropriate to bring all the volumes into best alignment. The other is a
new set of displacement vectors for each volume, so that when each volume is
independently warped with these vectors, adjacent volumes will be locally aligned
in their overlap zones. Further details about this program can be found at http://
bio3d.colorado.edu/imod/doc/man/stitchalign.html.
Options to this program include: stretch, to find in-plane stretch parameters;—
mag, to find overall magnification;—thin, to find factors by which to change the
thickness of the volumes;—size, to set the size in X and Y of transformed files to be
created by the volume warping program, Warpvol. The default is the size of the
largest input volume.
4.8.8 Tomostitch
Tomostitch is run to perform the final steps in stitching together the overlapping
volumes. Further details about this program can be found at http://bio3d.colorado.
edu/imod/doc/man/tomostitch.html. It is usually used in two stages, first to run
Findwarp on the warping vector fields produced by Stitchalign. If there are large
errors, the program will stop and the user will need to go back and edit more vectors
to improve the model. Then Tomostitch is run again to warp the volumes individually, stack them into a single montage volume with appropriate overlap, and
blend the pieces together to form the final supermontage volume.
This last step produces a binned supermontage that the user can open to evaluate
the quality of the lateral edge stitching. If the results are satisfactory, a full resolution supermontage can then be created; the result is a seamless, lateral stitching of
the individual montage panels to create the super-montage volume (Fig. 4.7d).
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E. O’Toole et al.
The Fitpatches tool assesses the quality of the patch displacements, and creates a set of
vector models that allow the user to manually correct aberrant vectors. Details about
this program can be found at http://bio3d.colorado.edu/imod/doc/man/fitpatches.html.
The program creates a number of vector models that can be opened and aberrant
vectors or ones with large residual values can be deleted. A description of the editing
process can be found in Sect. 12.5 of the IMOD Tomography Guide (http://bio3d.
colorado.edu/imod/doc/tomoguide.html). If models are edited, Fitpatches is run again
to convert the corrected vector models back into text files with displacements.
4.8.7 Stitchalign
The Stitchalign tool takes the edge vectors from Edgepatches or Fitpatches and
calculates two components needed for the final alignment. One is a set of linear
transforms appropriate to bring all the volumes into best alignment. The other is a
new set of displacement vectors for each volume, so that when each volume is
independently warped with these vectors, adjacent volumes will be locally aligned
in their overlap zones. Further details about this program can be found at http://
bio3d.colorado.edu/imod/doc/man/stitchalign.html.
Options to this program include: stretch, to find in-plane stretch parameters;—
mag, to find overall magnification;—thin, to find factors by which to change the
thickness of the volumes;—size, to set the size in X and Y of transformed files to be
created by the volume warping program, Warpvol. The default is the size of the
largest input volume.
4.8.8 Tomostitch
Tomostitch is run to perform the final steps in stitching together the overlapping
volumes. Further details about this program can be found at http://bio3d.colorado.
edu/imod/doc/man/tomostitch.html. It is usually used in two stages, first to run
Findwarp on the warping vector fields produced by Stitchalign. If there are large
errors, the program will stop and the user will need to go back and edit more vectors
to improve the model. Then Tomostitch is run again to warp the volumes individually, stack them into a single montage volume with appropriate overlap, and
blend the pieces together to form the final supermontage volume.
This last step produces a binned supermontage that the user can open to evaluate
the quality of the lateral edge stitching. If the results are satisfactory, a full resolution supermontage can then be created; the result is a seamless, lateral stitching of
the individual montage panels to create the super-montage volume (Fig. 4.7d).
112
E. O’Toole et al.