findgradient(1) General Commands Manual findgradient(1)
NAME
findgradient - Finds mag gradient that minimize montage blending error
SYNOPSIS
findgradient [options]
DESCRIPTION
Findgradient finds parameters related to magnification gradients that
minimize the displacement errors when Blendmont shifts pieces into reg-
istration. When the illumination in the microscope produces a signifi-
cant gradient in magnification with changing Z height, montages taken
at high tilt do not fit together well. The error in the overlap zones,
after shifting pieces into registration, can be several pixels. Cor-
recting for the gradient can reduce the error to a fraction of a pixel.
Thus, the parameters of the gradient can be found by adjusting them to
give minimum error. The two gradient parameters are the percent change
in magnification and the degrees of rotation per micron of Z height
change. The other parameter that affects the Blendmont error is the
effective tilt angle for the corrections, which can differ from the
nominal tilt angle by several degrees.
Findgradient can be run in three different modes, corresponding to the
number entered with the SearchType option. Two of these modes would be
used when measuring mag gradients from a set of calibration montages,
and the third would be used to adjust the tilt angles for an individual
tilt series to give optimum correction.
For calibrating gradients, it is recommended that montages be taken at
a single intensity at extreme positive and negative tilt angles (e.g.,
-60, -50, 50, and 60 degrees). Then montages would be taken at one
extreme angle and a series of intensities. The first step in the anal-
ysis would be to run Findgradient on the sections taken at the same
intensity and over a range of angles, computing the error from all of
those sections together and searching for both the magnification gradi-
ent and the best offset to the tilt angle (SearchType 3, RunSeparately
0). Then take the tilt offset from the search and specify it in the
OffsetTilts entry, and search for the magnification gradient separately
for all of the sections at the extreme angle (SearchType -2, RunSepa-
rately 1).
To find the best tilt offset for an individual tilt series once the mag
gradients have been calibrated, select two or three views from each end
of the tilt series. Select views where Blendmont does not have any
difficulty finding the displacements in the overlap zones, which may
not be the case at the very highest tilt. Run Findgradient to analyze
all of these sections together and search for the tilt offset only
(SearchType -1 or 1, RunSeparately 0). The mag gradient file must also
be specified with GradientFile.
At the end of the search for each section or group of sections, the
program prints a summary of the number of iterations in the search, the
final error, and the gradient values. The latter values are in addi-
tion to any initial gradient specified by a gradient file, so they
would be entered into Blendmont with the AddToGradient option.
Some of the options to Findgradient are passed directly to Blendmont.
If there are additional options that need to be used when running
Blendmont, they can be specified with BlendOption entries.
OPTIONS
Findgradient uses the PIP package for input exclusively (see the manual
page for pip). 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.
-imin (-imi) OR -ImageInputFile File name
Montaged image input file to be analyzed
-plin (-pl) OR -PieceListInput File name
File with list of piece coordinates for image input file.
-rootname (-r) OR -RootNameForFiles Text string
Root name for temporary files. The program will append -fg and
the starting and ending section numbers to create the full root
name. This name is used for the input parameter file (.param),
files for image output and text output from Blendmont (.imtmp
and .out), and the files created by Blendmont for edge functions
(.xef, .yef) and edge correlations (.ecd).
-distort (-d) OR -DistortionField File name
Image distortion field file to use for undistorting images. The
undistortion is applied when computing edge functions.
-imagebinned (-ima) OR -ImagesAreBinned Integer
The current binning of the images, so that the image distortion
field can be applied correctly. This entry is required when
doing image distortion corrections unless the program can deter-
mine the binning unambiguously from the image size.
-gradient (-gr) OR -GradientFile File name
File with magnification gradients for each section; the mini-
mization will determine the amounts to be added to these gradi-
ents. This should be a file listing the tilt angle, the percent
magnification change per micron of Z height, and the degrees of
rotation per micron of Z height for each section, such as is
produced by Extractmaggrad.
-adjusted (-adj) OR -AdjustedFocus
Focus was adjusted for changing Z height when montage was
acquired
-addgrad (-add) OR -AddToGradient Two floats
This option provides starting values for the minimization. The
reported gradient is not incremental to these values, unlike
when a gradient file is entered. The magnification gradient
correction is specified by two parameters: % of mag change per
micron of Z height, and degrees of rotation per micron of Z
height. If -gradient has been entered, the values entered here
will be treated as incremental to the values in the gradient
file for each section. If -gradient has not been entered, the
values entered here will be used for all sections; but in this
case the -geometry option must be entered to provide additional
information.
-geometry (-ge) OR -TiltGeometry Three floats
This entry can be used in place of a gradient file to specify
the pixel size in nanometers, tilt axis rotation angle, and tilt
angle to be used for the gradient computation. The entry has no
effect if a gradient file is provided.
-tiltfile (-ti) OR -TiltFile File name
Name of file with tilt angles, one per line. These angles will
be used only if there is no mag gradient file to supply the tilt
angles.
-offset (-o) OR -OffsetTilts Floating point
Add the given value to the tilt angles from the gradient file or
the tilt file. For a search of 1 or 3 parameters, this value
will be used as the starting value for finding the best offset.
-sections (-sec) OR -SectionsToDo List of integer ranges
List of sections on which to minimize overlap errors; comma-sep-
arated ranges are allowed. The mean error over all of these
sections will be minimized unless the -separate option is
included, in which case the procedure is run separately on each
section.
-separate (-sep) OR -RunSeparately
Run minimization separately on each section, instead of combin-
ing the errors from all sections. With this option, the list of
sections must be specified with -sections.
-search (-sea) OR -SearchType Integer
Enter 1 or -1 to find just the tilt offset with a fixed mag gra-
dient, 2 or -2 to find the mag gradient with a fixed tilt off-
set, and 3 to find both the mag gradient and the best tilt off-
set. The latter should be used only when multiple sections with
a big difference in their tilt angles are searched together (not
separately). The positive values do a search with a simplex
algorithm. Use -2 to find gradients with a routine that uses an
estimated gradient from Blendmont to modify the gradient until
it converges. This method is faster and seems to be slightly
more reliable. Use -1 to search for the tilt offset with a sim-
ple routine that is faster and probably as reliable as the sim-
plex routine.
-trace (-tr) OR -TraceOutput Integer
Output values during minimization: 1 for minima, 2 for all val-
ues
-blend (-b) OR -BlendOption Text string
Option and value to pass to Blendmont. This option will be
added the end of the .param file. There is no check for whether
options entered this way conflict with the options placed into
the .param file by findgradient. (Successive entries accumu-
late)
-param (-pa) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input.
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 findgradient(1)