#tomoauto
tomoauto is a wrapper-library written in Lua to automate the alignment, correction and recontstruction of cryo-electron tomography (Cryo-ET) tilt-series. Coupled with high-throughput collection, tomoauto speeds up data processing so that more time can be spent on data analysis.
tomoauto is simply a script that handles the use of several popular software packages in the field and simplifies their use in collection by globalizing the command line calls and configuration. It has been running in some form or fashion in our lab for the last 3 years with good results.
Recent releases have expanded the original functionality to handle direct detector cameras, dose-fractionation, and more complex operations on MRC files.
- A really big overhaul that reorganized most of the libraries.
- mrcio.lua is now handled in an object oriented manner to make interactive user use more friendly.
- Settings have been broken up and placed in their own folder to make editing global configuration more easy, and it is now also in a standard format using lua tables to make the syntax a little easier to remember and read.
- Every option for every command handled by tomoauto is now in the settings.
- Added mdoc support, hopefully in the future we will move to just handling
mdocs and not MRC files or logs for
dose_fractioned_to_stack. - Added some transform routines, they're not in use right now but will be used later on to do some conversions from I3 to dynamo in terms of orientations and such.
- Update for Lua 5.3.0 release
- Added a CTF test-suite comparing CTFFIND4 and CTFPLOTTER
- Added programs to handle motion-correction with MOTIONCORR
- No longer need struct library
- bit32 library was deprecated and therefore removed
- Wrote a new installation script and packaged with sources for lua and needed Lua libraries.
- Changed final files kept to save space and rely on options available in 3dmod
- As of IMOD 4.7.9 autofidseed works better than RAPTOR to generate the fiducial seed model and is now default. RAPTOR can still be used by passing the appropriate option (see tomoauto --help).
- Added mode option to stop at alignment, ccderase, or to only perform reconstruction
- Stopped using RAPTOR to generate the alignment, now it only produces the fiducial seed model and then IMOD performs the alignment.
- No longer using a folder with the basename which helps keep things clean and organized when using the align and then the reconstruct mode.
- Removed all batch commands, handle them yourself with the shell.
- Added programs to create a newstack from drift-corrected images collected by dose-fractionation.
- Added a pretty substantial lua module to handle MRC files.
- Most of the IMOD commands handle multi-core automatically so removed -p option.
[TOMO3D] (https://sites.google.com/site/3demimageprocessing/software)
[CTFFIND4] (http://grigoriefflab.janelia.org/ctffind4)
[MOTIONCORR] (http://cryoem.ucsf.edu/software/driftcorr.html)
If you use this software please read the license file and use the software appropriately. Also there are many papers to cite if you use this software in your research.
IMOD:
Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76.
Mastronarde, D. N. (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120:343-352.
RAPTOR
F. Amat, F. Moussavi,L.R. Comolli, G. Elidan, K.H. Downing, M. Horowitz (2008) "Markov random field based automatic image alignment for electron tomography". J. Struct. Biol. 161: 260-275
TOMO3D
J.I. Agulleiro, J.J. Fernandez (2011) Fast tomographic reconstruction on multicore computers. Bioinformatics 27:582–583.
J.I. Agulleiro, E.M. Garzon, I. Garcia, J.J. Fernandez. (2010) Vectorization with SIMD extensions speeds up reconstruction in electron tomography. J. Struct. Biol. 170:570-575.
J.I. Agulleiro, J.J. Fernandez. (2012) Evaluation of a multicore-optimized implementation for tomographic reconstruction. PLoS ONE 7(11):e48261.
CTFFIND4
J.A. Mindell, N. Grigorieff. (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142(3):334-47.
doi:10.1016/S1047-8477(03)00069-8
MOTIONCORR
X. Li, et al. (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10(6):584-90.
[doi: 10.1038/nmeth.2472](http://dx.doi.org/doi: 10.1038/nmeth.2472)
See INSTALL file. Place the tomoauto directory where you want to install it and in that directory run install_tomoauto.sh.