transferfid
transferfid(1) General Commands Manual transferfid(1)
NAME
transferfid - make seed model for second axis from fiducials for first
axis
SYNOPSIS
transferfid [options] setname
DESCRIPTION
transferfid will make a seed model for tracking fiducials in one axis
of a dual-axis tilt series, using the fiducial model for the other
axis. It first finds a pair of views from the two axes that match up
well after an appropriate translation, rotation, and stretching of the
view from the first axis. It then transforms the corresponding section
of the fiducial model from the first axis by the same amount, and uses
Beadtrack to find each bead on the view from the second axis. This
collection of new positions then forms the seed model for tracking the
second axis.
The program will do all of these operations without any arguments
except the name of the data set if all files are named appropriately;
specifically, if the command files for beadtrack are named tracka.com
and trackb.com, and the tilt angles are in files with extension
.rawtlt. By default, the program will transfer fiducials from the "a"
axis to the "b" axis, in which case it assumes the first fiducial model
is named setnamea.fid. However, you can use the -b option to transfer
from the "b" axis to the "a" axis, in which case the existing fiducial
model is assumed to be named setnameb.fid. By default, the program
will search for the best matching pair of views using the 5 views near-
est to zero tilt from each data set. It will consider rotations by
both -90 and +90 degrees, and it will set the bead radius for Beadtrack
using the value in tracka.com.
Pixel sizes in the image file headers are assumed to be accurate. If
they differ, the program will issue a warning but try to proceed by
scaling the images from the first axis by the ratio of pixel sizes.
If the program fails to find the proper alignment between the two axes,
this is probably because the rotation is too far from 90 degrees,
and/or the translations are too large. If the rotation is too far off,
you can try entering the -scan opton with a larger range to search.
Otherwise, you can solve this problem by using the -m option to run
midas and set the initial rotational and translational alignment
manually. When you get into Midas, you may need to rotate the image by
180 degrees, unless you specify the angle in advance with the -a
option, but this large rotation will not cause problems. If you find
that the images are mirror images of each other, then you can either
mirror one around the X axis in Midas using the entry in the Edit menu,
or go back to running Transferfid without Midas but with the -x option.
Once the seed model is created, the program analyzes contours in the
fiducial model from the first axis to provide information that is
needed when running solvematch. If the -c option is used, then cor-
responding coordinates of the transferred beads in the two data sets
will be placed into the specified output file. This information is
sufficient for solvematch to identify the corresponding fiducials in
the final alignment, regardless of whether some seed points fail to
track or some contours are deleted from either fiducial model. If this
option is not used, the program indicates what the correspondence
between points should be when running solvematch. The list of
points in A could be in error in some cases unless a fiducial coordi-
nate file (setnameafid.xyz) is also available. For this reason, it is
advisable to run tiltalign at least once on the first fiducial model
before running transferfid. The lists could also become erroneous if
one of the points in the new seed model fails to track, or if fiducials
are deleted from either model after running transferfid. If such
changes occur, just enter a small starting subset of points and let
solvematch come up with the rest of the correspondences.
Finding the best pair of views is somewhat time-consuming. Two ways to
reduce this time are to reduce the number of views in the search with
the -n option and to specify the direction of rotation between the axes
with the -a option. The latter option alone will save only 15% of the
time, because the program will abandon one rotation direction if it is
clearly worse after considering four pairs of views, or only two if the
difference between directions is very large.
OPTIONS
Transferfid uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-s OR -Setname Text string
Root name of dataset (omit the a or b)
-b OR -TransferBtoA
Transfer backwards, from the "b" axis to the "a" axis. You will
generally not need to specify any filenames with this option.
-ia OR -AImageFile File name
Set the name of the image file upon which the fiducial model for
the "a" axis tilt series was built; the default is to take the
name from the tracka.com command file.
-ib OR -BImageFile File name
Set the name of the image file for tracking beads in the "b"
axis tilt series; the default is to take the name from the
trackb.com command file.
-f OR -FiducialModel File name
Set the name of the fiducial model file for the first, already
tracked tilt series; the default is setnamea.fid (or set-
nameb.fid with the -b option.)
-o OR -SeedModel File name
Set the name of the output file for the seed model; the default
is setnameb.seed (or setnamea.fid with the -b option.)
-boundary (-bo) OR -BoundaryModel File name
Model file with boundary contours around areas to correlate in
the A stack, which will be transformed to fit the B stack. The
program will find the best matching pair of views in the image
stacks, and then transform this model appropriately instead of
trying to transfer seed points. The fiducial model file need
not exist. If the file name does not begin with "setnamea" (or
"setnameb" with the -b option), the -o option must be entered
with an output file name.
-n OR -ViewsToSearch Integer
Set the number of views from each data set to include in the
search for the best matching pair of views; the default is 5.
-za OR -ACenterView Integer
Set the number of the view from the "a" axis tilt series around
which to search for the best match; the default is the view
nearest to zero tilt, using tilt angles in the file set-
namea.rawtlt or tilt angles implied by FirstTiltAngle and Tilt-
Increment entries in tracka.com.
-zb OR -BCenterView Integer
Set the number of the view from the "b" axis tilt series around
which to search for the best match; the default is the view
nearest to zero tilt, using tilt angles in the file set-
nameb.rawtlt or tilt angles implied by FirstTiltAngle and Tilt-
Increment entries in trackb.com.
-a OR -AngleOfRotation Integer
Use this option to specify the direction of rotation from the
first to the second axis. Only the sign of this number matters,
so you can enter -1 or -90 for clockwise rotations, or 1 or 90
for counterclockwise rotations. In the absence of this option,
the program will consider both directions of rotation.
-x OR -MirrorXaxis Integer
This option controls whether the image from one stack is mir-
rored around the X axis before rotating by 90 degrees. Enter 1
to mirror always, -1 to never mirror, or 0 to have the program
assess both with and without mirroring. The default is 0.
-m OR -RunMidas
Run Midas on the first pair of views, and use the alignment that
you set in Midas as the initial alignment for all pairs of views
that are considered.
-scan (-sc) OR -ScanRotationMaxAndStep Two floats
Either the maximum angle and angular step size at which to apply
rotation in order to estimate the best rotation; or a single
rotation angle to apply and a 0 step size; or 0,0 for no rota-
tion scan (legacy behavior). In the latter case, or when the
rotation scan finds the best rotation at the end the range, an
initial run of Xfsimplex will be done to search for rota-
tion/translation only. The default is 20 and 4, which will
accommodate inaccuracies in 90-degree rotation of up to ~22
degrees, and give fairly accurate interpolated rotation values
that allow the first Xfsimplex step to be skipped.
-c OR -CorrespondingCoordFile File name
Use this option to have corresponding fiducial coordinates on
the best matching views placed into an output file. This file
will also record the section numbers in the two sets and whether
the transfer was from "b" to "a".
-lowest (-l) OR -LowestTiltTransformFile File name
File in which to save transform for lowest tilt pair of views
-t OR -LeaveTempFiles
For diagnosing problems, leave temporary files in the standard
temporary directory (/usr/tmp, /tmp, or defined by IMOD_TMPDIR)
or in the current directory if there is no temporary directory.
-PID Print process ID
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
Whether or not they fit the default naming conventions, the image files
for fiducial tracking for each tilt series and the first fiducial model
must be present in the current directory. If the output file already
exists, a backup image of the original is created with the ~ extension.
AUTHOR
David Mastronarde <mast at colorado dot edu>
SEE ALSO
beadtrack, tiltxcorr, remapmodel, clipmodel, xfsimplex,
xfmodel, midas, solvematch, tiltalign
IMOD 5.2.0 transferfid(1)