[3dem] AreTomo3 - live cryoET preprocessing pipeline released

[Shawn Zheng]

Dear Colleagues,

I am delighted to announce that we have reached another milestone in our
journey to promote cryoET and subtomogram averaging for in situ structural
determination. AreTomo3, a live preprocessing pipeline, has been officially
released. It is open source and can be downloaded at
https://urldefense.com/v3/__https://github.com/czimaginginstitute/AreTomo3__;!!Mih3wA!ERxgaptMme28k5nCSY9N0i0bBH7U150qcRtiq_RmMuVXXfJnqBzoUCdxVWFAZBBH_FVsfEcu5riW4OaXzIXd90s$ . The following is a brief
intro of AreTomo3. We sincerely hope that you will find this package useful
and welcome any suggestions that are always appreciated.

Best regards,
Shawn Zheng

AreTomo3 is a multi-GPU accelerated software package that enables real-time
fully automated reconstruction of cryoET tomograms in parallel with cryoET
data collection. Integrating MotionCor3, AreTomo2, and GCtfFind in a single
application, AreTomo3 has established an autonomous preprocessing pipeline
that, whenever a new tilt series is collected, can activate and repeat
itself from correction of beam induced motion and assembling tilt series to
CTF estimation and correction, tomographic alignment, and 3D reconstruction
throughout entire session of data collection without human intervention.
The end results include not only tomograms but also a rich set of alignment
parameters to bootstrap subtomogram averaging. Our test shows that AreTomo3
can catch up to 9-target PACE Tomo data collection with 4 NVidia RTX A6000
GPUs when it was configured to perform 2D local motion correction on movies
and 3D local motion correction on tilt series. The offline testing shows
that AreTomo3 runs faster than the data collection. As a result, GPU
resources can be shared with other tasks to expand the preprocessing
capacity. Tomogram denoising and particle picking now can run concurrently
with AreTomo3 to maximize the preprocessing workflow.
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