cAligner

3D alignment of cryo electron tomographic tilt series using Google's Ceres for non-linear least squares optimization.

Based on the Artiatomi package for processing cryo-tomography data. Using the acquisition model described in:

Castaño-Díez, D., Seybert, A., Frangakis, A.S. (2006). Tilt-series and electron microscope alignment for the correction of the non-perpendicularity of beam and tilt-axis. Journal of Structural Biology.

Uses getoptpp for command line input.

Dependencies

• Ceres 1.14 (installation guide)

Build

cAligner can be built using cmake.

git clone https://github.com/uermel/cAligner.git
cd cAligner
mkdir build
cd build
cmake ..
make

Usage

$ ./cAligner --help
cAligner aligns tomographic tilt series based on fiducial marker positions on the projection images.

Usage:
	cAligner -input FILE -output FILE [OPTIONAL PARAMETERS]

I/O (required):
	-i; --input 		 Input filename.
	-o; --output 		 Output filename.

Alignment parameters:
	-a; --activeMarker 	 Marker to center alignment around (default 0).
	-w; --width 		 Projection width in pixels (default 7420).
	-h; --height 		 Projection height in pixels (default 7676).
	--maAmount 		 Magnification Anisotropy amount (default 1).
	--maAangle 		 Magnification Anisotropy angle in degrees (default 0).
	--phi 			 Beam declination angle in degrees (default 0).
	--iter 			 Number of iterations to run (default 20).
	--iterSwitch 		 Iteration after which to switch between theta/mags (default 10).
	--zShift 		 Additional z-shift applied during alignment.

Alignment types:
	--doPsi 		 Align for image rotation.
	--doFixedPsi 		 Keep image rotation constant for all projections.
	--doTheta 		 Align tilt angles.
	--doPhi 		 Align for beam declination.
	--doMags 		 Align for magnification change.
	--normMin 		 Normalize mag change by minimum value
	--normZeroTile 		 Normalize mag change by 0-deg projection
	--magsFirst 		 Align for mag change first, then tilt angles