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TiltRec

Introduction

TiltRec is an efficient software tool for cryo-electron tomography reconstruction using MPI and CUDA.

System Requirements and Dependencies

  • CMake: Version 2.6 or newer.
  • MPICH
  • CUDA: A minimum of version 11 is required to leverage GPU acceleration for computations.
  • OpenCV4
  • Docker(optional)

Compilation Instructions

Without Docker

mkdir build
cd build
cmake ..
make -j8

Using Docker

docker build -t tiltrec:v1 .
docker run -it --rm --gpus all tiltrec:v1 /bin/bash
mkdir build
cd build
cmake ..
make -j8

Command-Line Options

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]

Parameters

  • -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.

Example

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

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