RAPTOR(1) General Commands Manual RAPTOR(1)
NAME
RAPTOR - Automatic alignment of tilt series with fiducial markers
SYNOPSIS
RAPTOR [options]
DESCRIPTION
RAPTOR (Robust Alignment and Projection Estimation for Tomographic
Reconstruction) aligns tomographic tilt series obtained from electron
microscopes. It is intended to automatically obtain a full-precision
alignment comparable to the one obtained with extended manual interven-
tion. Fiducial particles are needed in the image for the alignment.
RAPTOR has been tested in many different datasets (cryo-EM, plastic,
thick sections) and has given very good results. However, any feed-
back, questions, or suggestions will be greatly appreciated.
RAPTOR was developed primarily by Fernando Amat and Farshid Moussavi
while they were at Stanford University. They have contributed it for
incorporation into IMOD and still maintain and develop it.
If you use RAPTOR in your research, please cite the following paper:
F. Amat, F. Moussavi,L.R. Comolli, G. Elidan, K.H. Downing, M.
Horowitz. "Markov random field based automatic image alignment for
electron tomography". Journal of Structural Biology , March 2008, pages
260-275.
Inside IMOD, RAPTOR is run by Etomo using a wrapper script, "runrap-
tor". This script must be run from inside the data directory where a
reconstruction is being done. It takes care of adding the -exec,
-path, -input, -track, and -output options, and it passes other options
through to RAPTOR. It requires that the -diam and -mark options be
entered. It places output in a numbered series of subdirectories,
"raptor1", "raptor2", etc. if it is run multiple times. It takes care
of making an IMOD model that can be loaded onto the image stack in
3dmod.
OPTIONS
RAPTOR 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.
-execPath (-e) OR -RaptorExecPath Text string
Path where RAPTOR binaries are located (required)
-path (-p) OR -InputPath Text string
Path where MRC stack to be aligned is located (required)
-input (-i) OR -InputFile File name
Input filename, without the path (required)
-output (-ou) OR -OutputPath Text string
Path where output files will be saved (required)
-diameter (-d) OR -Diameter Multiple integers
Diameter(s) of the markers, in pixels. If you bin the image
with with the -bin option to RAPTOR, the diameter has to be the
one in the original image indicated by the -input entry, NOT the
binned one. If the dataset has more than one kind of marker just
specify the different sizes separated by commas. This entry is
required.
-white (-w) OR -WhiteMarkers
Search for markers that have higher values than the background
in the MRC stack (like quantum dots or images with inverted con-
strast).
-markers (-mar) OR -MarkersPerImage Integer
Number of markers to be tracked. THIS IS A CRITICAL PARAMETER.
If Raptor fails aligning the stack try increasing this number
(it will just make the run slower). We have develop a method to
try to estimate this parameter automatically. If you don't spec-
ify a number, RAPTOR will perform an estimation.
-angles (-a) OR -AnglesInHeader
If this option is specified, RAPTOR will extract tilt angles
from the header of the input stack. Otherwise, it will expect
to find tilt angles in a ".rawtlt" file.
-bin (-b) OR -Binning Integer
With this option, RAPTOR will bin the stack before performing
alignment. Remember that binning affects the diameter of the
markers.
-rec (-re) OR -Reconstruction Integer
If this option is specified, RAPTOR will run IMOD's Tilt pro-
gram after alignment to perform the 3D reconstruction. The
entry must be 0,1 or 2 to indicate the mode of the reconstruc-
tion (0 for byte, 1 for signed integer, 2 for float).
-thickness (-th) OR -Thickness Integer
Thickness of the tomogram, if -rec option is entered
-orientation (-or) OR -Orient Integer
This option controls the handedness of a tomogram generated by
the CalTech version of RAPTOR (not the one in IMOD). Enter -1
to use the PARALLEL option when running Tilt, which inverts
handedness; the default is to use the RotateBy90 option.
-tracking (-tr) OR -TrackingOnly
If this option is specified, RAPTOR does not generate an aligned
stack or reconstruction. It just returns a fiducial model with
all the tracked trajectories, like the bead tracker in IMOD.
-xray (-x) OR -xRay
If the images contain strong straight line features (such as
edges of a capillary sample holder) they will affect the marker
detection process. Enter this option in order to remove these
strong features and improve marker detection performance.
-verb (-v) OR -Verbose Integer
Specify how much output RAPTOR should write and keep:
0 for minimal output. Only reconstructed volume and a minimal
log file are kept
1 for standard output (the default). Aligned stack is kept as
well as fiducial model for IMOD and log with RAPTOR's progress.
2 for debug mode. RAPTOR writes an extended output log as well
as status in intermediate steps of the process. Useful to report
and detect errors.
Advanced Options
Use these options only if you have a good understanding of the algo-
rithm parameters.
-maxDist (-max) OR -MaxDistanceCandidate Integer
Maximum distance between two markers in adjacent projections for
them to be considered as possibly the same marker in each sepa-
rate projection.
-minNeigh (-mi) OR -MinNeighborsMRF Integer
Minimum number of neighbors per marker to build the graphical
model when solving for the correspondence problem.
-rollOff (-ro) OR -RollOffMRF Integer
Coefficient of the exponential decay to penalize markers that
are far away when establishing correspondences between projec-
tions
-seed (-s) OR -Seed Integer
Seed for Pseudo-random generator; supplying this allows RAPTOR
to generate identical results when run on the same data.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
Output
In the folder specified as output you will find the following subfold-
ers: IMOD, align, temp and debug (if the option "-verb 2" was speci-
fied).
A. align folder: contains an aligned stack (*.ali), a RAPTOR report of
execution (*_RAPTOR.log), and a report of IMOD commands executed within
RAPTOR (*_IMOD.log). If you specified -rec it will contain the tomogram
as well (*.rec)
B. IMOD folder: contains a final fiducial model (*.fid.txt), the align
script used to generate an aligned stack (*_tiltalignScript.txt), and
final refined tilt angles (*.tlt).
Note: you can use the original stack (input file or binned file in case
you specified -bin) and the fiducial model *.fid.txt to check if the
fiducial tracking was successful. Just open both the model and stack
with 3dmod to visualize. You can also correct the model. To create
a new aligned stack just run tiltalign -param *_tiltAlignScript.txt
from the output/IMOD folder.
C. debug folder: if -verb 2 was specified it contains intermediate
files to check RAPTOR performance. For example, it contains the tem-
plate used to detect markers or fiducial models at different steps of
the program.
AUTHORS
Fernando Amat and Farshid Moussavi
SEE ALSO
3dmod, tilt, tiltalign
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 RAPTOR(1)