AreTomo2 is a multi-GPU accelerated software package that automates motion-corrected marker-free tomographic alignment and reconstruction. It includes robust GPU-accelerated CTF estimation, offering fast, accurate, and easy integration into subtomogram processing workflows. AreTomo2 is capable of on-the-fly reconstruction of tomograms and CTF estimation in parallel with tilt series collection, enabling real-time sample quality assessment and collection parameter adjustments.
Tags
templatejavaimagej2scijava
Citation
Zheng, S., Wolff, G., Greenan, G., Chen, Z., Faas, F.G., Bárcena, M., Koster, A.J., Cheng, Y. and Agard, D.A., 2022. AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. Journal of Structural Biology: X, 6, p.100068.https://github.com/czimaginginstitute/AreTomo2
Solution written by
Kyle Harrington
License of solution
MIT
Arguments
--InMrc
Input MRC file that stores the tomographic tilt series. (default value: PARAMETER_VALUE)
--OutMrc
Output MRC file that stores the aligned tilt series. (default value: PARAMETER_VALUE)
--AlnFile
Alignment file to be loaded and applied to the loaded tilt series. (default value: PARAMETER_VALUE)
--AngFile
Text file containing tilt angles. Must match the number and order of projection images in the input MRC file. (default value: PARAMETER_VALUE)
--TmpFile
Temporary image file for debugging. (default value: PARAMETER_VALUE)
--LogFile
Log file storing alignment data. (default value: PARAMETER_VALUE)
--TiltRange
Min and max tilts. By default, the header values are used. (default value: PARAMETER_VALUE)
--TiltAxis
Tilt axis, default header value. (default value: PARAMETER_VALUE)
--AlignZ
Volume height for alignment, default 256 (default value: PARAMETER_VALUE)
--VolZ
Volume z height for reconstruction. Must be greater than 0 to reconstruct a volume. Default is 0, only aligned tilt series will be generated. (default value: PARAMETER_VALUE)
--OutBin
Binning for aligned output tilt series, default 1 (default value: PARAMETER_VALUE)
--Gpu
GPU IDs. Default 0. (default value: PARAMETER_VALUE)
--TiltCor
Correct the offset of tilt angle. Can be followed by two values for specifying offset adjustment in alignment and/or reconstruction. (default value: PARAMETER_VALUE)
--ReconRange
Specifies the min and max tilt angles for 3D volume reconstruction. Excludes tilt images outside this range in the reconstruction. (default value: PARAMETER_VALUE)
--PixSize
Pixel size in Angstrom of the input tilt series, required for dose weighting. If missing, dose weighting is disabled. (default value: PARAMETER_VALUE)
--Kv
High tension in kV, required for dose weighting and CTF estimation (default value: PARAMETER_VALUE)
--ImgDose
Dose on sample in each image exposure in e/A2. Not the accumulated dose. If missing, dose weighting is disabled. (default value: PARAMETER_VALUE)
--Cs
Spherical aberration in mm, required only for CTF correction (default value: PARAMETER_VALUE)
--$-10s
Amplitude contrast, default 0.07 (default value: PARAMETER_VALUE)
---10s
Guess of phase shift and search range in degree, required for CTF estimation with a phase plate installed. (default value: PARAMETER_VALUE)
--FlipVol
If non-zero, the reconstructed volume is saved in xyz fashion. Default is xzy. (default value: PARAMETER_VALUE)
--FlipInt
Flip the intensity of the volume. Default 0 means no flipping. Non-zero value flips. (default value: PARAMETER_VALUE)
--Sart
Specify number of SART iterations and number of projections per update. Default values are 15 and 5, respectively. (default value: PARAMETER_VALUE)
--Wbp
If specified as 1, enables weighted back projection for volume reconstruction. (default value: PARAMETER_VALUE)
--DarkTol
Set tolerance for removing dark images. Range is (0, 1), default 0.7. Higher value is more restrictive. (default value: PARAMETER_VALUE)
--TiltScheme
Determines sequence of tilt image acquisition, needed for accumulated dose determination. Three parameters required: starting angle, tilt step, and collection scheme (1, 2, or 3). (default value: PARAMETER_VALUE)
--OutXF
If set to a non-zero value, generates an IMOD compatible XF file. (default value: PARAMETER_VALUE)
--OutImod
Generates Imod files needed by Relion4 or Warp for subtomogram averaging. Saved in a subfolder named after the output MRC file. (default value: PARAMETER_VALUE)
--Align
Skip alignment if set to 0. Used when the input MRC file is an aligned tilt series. Default is 1. (default value: PARAMETER_VALUE)
--CropVol
Crop the reconstructed volume to specified sizes in x and y directions. Enabled only when -RoiFile is enabled. (default value: PARAMETER_VALUE)
--Bft
B-factors for low-pass filter used in cross correlation. First value for global measurement, second for local measurement. (default value: PARAMETER_VALUE)
--IntpCor
Enables correction for information loss due to linear interpolation. Default setting value 1 enables the correction. (default value: PARAMETER_VALUE)