TiltRec is an efficient software tool for cryo-electron tomography reconstruction using MPI and CUDA.
- CMake: Version 2.6 or newer.
- MPICH
- CUDA: A minimum of version 11 is required to leverage GPU acceleration for computations.
- OpenCV4
- Docker(optional)
mkdir build
cd build
cmake ..
make -j8
docker build -t tiltrec:v1 .
docker run -it --rm --gpus all tiltrec:v1 /bin/bash
mkdir build
cd build
cmake ..
make -j8
TiltRec provides a variety of command-line options to allow users more flexibility when running cryo-ET reconstructions. The basic command-line structure is as follows:
mpirun -n p ./TiltRec [options]
-
-INPUT(-i) <input filename>
:The name of the input MRC file used for reconstruction. -
-OUTPUT(-o) <output filename>
: Designates the name of the resulting MRC file. -
-TILTFILE(-t) <tilt angle filename>
: The file containing tilt angles for the reconstruction. -
-INITIAL <initial reconstruction filename>
: Provides an initial MRC file to be used as the model for iterative reconstruction methods (optional). -
-GEOMETRY(-g) <4 integers>
: Defines geometric information: offset, pitch angle, z-axis offset, and thickness. -
-AXIS <reconstruction axis>
: Sets the axis for reconstruction, either y (default) or z. -
-METHOD(-m) <method name>
: Selects the reconstruction method:- Back Projection :BPT
- Filtered Back Projection: FBP
- Weighted Back Projection: WBP
- SART: SART, number of iterations, relaxation parameter
- SIRT: SIRT, number of iterations, relaxation parameter
- ADMM: ADMM, number of iterations, number of conjugate gradient iterations, relaxation parameter, threshold
-
-help(-h)
: Displays help information.
The following example demonstrates how to perform a reconstruction using the Weighted Back Projection (WBP) method along the y-axis with two threads:
mpirun -n 2 ./TiltRec-cuda --input ../../data/BBb/BBb_fin.mrc --output ../../data/BBb/BBb_SIRT_y.mrc --tiltfile ../../data/BBb/BBb.rawtlt --geometry 0,0,0,300 --method WBP