Artiatomi

This is the official Artiatomi cryo electron tomography package

it consists of the following tools or applications:

• EmSART: The "main" tool, performing tomographic reconstruction of cryo-EM tilt series. It accepts DM3/4 file series or MRC/ST files as input and writes the result in one EM file. MRC output is also implemented but not well tested. Core of the implemented method is super-sampling SART and three- dimensional CTF correction. References:

  1. Kunz, M. & Frangakis, A.S. (2014). Super-sampling SART with ordered subsets. J Struct Biol. 2014 Nov;188(2):107-15.
  2. Kunz, M. & Frangakis, A.S. (2017). Three-dimensional CTF correction improves the resolution of electron tomograms. J Struct Biol. 2017 Feb;197(2):114-122.

  If you use EmSART for reconstruction of your EM data, please make sure to properly cite the methods used. If you develop software based on this implemantation, please also cite one of these papers. --> sub folder: EmSART

• EmSARTRefine: Finds the individual shift of each sub-volume on each tilt of the tilt-series. ref: Paper to be published sub folder: EmSART

• EmSARTSubVolumes: Reconstructs sub-volumes with weighted back- projection with three-dimensional CTF-correction without the need of reconstructing a full volume. Includes the individual shift information. sub folder: EmSART

• MarkerAlignator: A command line tool to align marker files, provided either as EM-file (old TOM-toolbox format) or a set of IMOD marker files (*.fid, *.tlt, *.prexg). In theory, one could also convert the final IMOD alignment files, but this turned out to be ambiguous due to post-processing in IMOD, why we prefer to align the tilt-series independently from the clicked positions in the micrographs. sub folder: EmTools/MarkerAlignator

• ImageStackAligntor: A command line tool to align dose- fractionation stacks. The first step consists of minimizing the consistency error of a shift-matrix (ref: Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM Xueming Li et al., Nat Methods. 2013 Jun; 10(6): 584–590.) followed by iterative re-aligning one frame to the sum of the other aligned frames until convergence. To avoid interpolation artifacts, we also search only for full-pixel shifts. sub folder: EmTools/ImageStackAlignator

• Clicker: A GUI tool to visualize tilt series and click gold beads. sub folder: Clicker

• SubTomogramAveraging: This application performs sub-tomogram averaging as done in the old TOM-toolbox, with full GPU acceleration and the capabilility to run on a compute cluster using MPI. sub folder: SubTomogramAverageMPI

Compilation:

All development was done on Windows and Visual Studio in varying versions. For Linux, each tool has a hand written make file for now. Some applications can be built using cmake.

Dependcies:

• Cuda 8.0
• openMPI on Linux, version of your choice
• MPICH on Windows, http://www.mpich.org/static/downloads/1.4.1p1/mpich2-1.4.1p1-win-x86-64.msi
• For Clicker only: Qt 5.5, we still have troubles to get that compiled on different machines...

Cuda kernels:

the kernels are mostly only compiled on Windows either through visualStudio or a batch file. The resulting ptx-file is then converted to a byte-array in a header file which is then used during compilation of the host-code, both for Windows and Linux. The main reason for this manual compilation step is the use of the CUDA driver API due to historic reasons.

Missing symbols while linking:

The same code is re-used for different tools (especially EmSART and its falvours) with different code segments enabled or disabled by pre-processor macros. If you encounter linking errors, run a "make clean" before the "make" step to correct for this.