Jul 01

Software for Time Interlaced Model Based Iterative Reconstruction (TIMBIR)


The time-interlaced model-based iterative reconstruction (TIMBIR) [1,2] is a method for 4D time-space reconstruction of data acquired using synchrotron X-ray computed tomography. TIMBIR is a synergistic combination of two innovations. The first innovation, interlaced view sampling, is a novel method of data acquisition which distributes the view angles more evenly in time. The second innovation is a 4D model-based iterative reconstruction algorithm (MBIR) which can produce time-resolved volumetric reconstruction of the sample from the interlaced views. In addition to modeling both the sensor noise statistics and the 4D object, the MBIR algorithm also reduces ring and streak artifacts by more accurately modeling the measurement non-idealities [1,2,3].

Software Highlights

  • Software for reconstruction of data acquired using parallel-beam X-ray tomography.
  • Performs 4D MBIR reconstruction using interlaced views.
  • Also supports conventional 3D MBIR reconstruction using progressive views (i.e., views with equi-angular steps).
  • It can also reconstruct data at any arbitrary set of angles by providing the angle list as an input.
  • Automatically produces ring and streak artifact free reconstructions.
  • Optimized to run in parallel on a super-computing cluster.
  • Also runs on a standard linux PC or MAC.
  • Includes examples for both 3D and 4D reconstruction.
  • Software is open-source and publicly available on github. Feedback and bug reports are welcome.

Software Requirements

  • MPI C/C++ compiler
  • OpenMP library
  • make utility

Software Links

The following link redirects to the github page for the 4D MBIR reconstruction software used in TIMBIR.

Download 4D MBIR


  1. K. A. Mohan, S. V. Venkatakrishnan, J. W. Gibbs, E. B. Gulsoy, X. Xiao, M. De Graef, P. W. Voorhees, and C. A. Bouman, "TIMBIR: A method for time-space reconstruction from interlaced views," IEEE Transactions on Computational Imaging.
  2. K. A. Mohan, S. V. Venkatakrishnan, J. W. Gibbs, E. B. Gulsoy, X. Xiao, M. De Graef, P. W. Voorhees, and C. A. Bouman, "4D model-based iterative reconstruction from interlaced views," accepted at IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP), April 2015.
  3. K. A. Mohan, S. V. Venkatakrishnan, L. F. Drummy, J. Simmons, D. Y. Parkinson, and C. A. Bouman, "Model-based iterative reconstruction for synchrotron X-ray tomography," in Acoustics, Speech and Signal Processing (ICASSP), 2014 IEEE International Conference on, May 2014, pp. 6909.6913.