[3dem] RELION-5 cryo-ET pipeline

[Sjors Scheres - MRC LMB]

Dear #teamtomo,

We are happy to announce that the new tomography pipeline in the 
beta-release of RELION-5.0 is now ready for general beta-testing.

The new pipeline comprises the import of raw movie frames and MDOC 
metadata files, motion correction (in RELION or UCSF MotionCor2), CTF 
estimation (in CTFFIND-4.1), visual inspection of tilt series images, 
tilt-series alignment (in IMOD or AreTomo), reconstruction of tomograms, 
manual picking of particles in a napari-based viewer, and the extraction 
of particles as 3D pseudo-subtomograms or as 2D particle stacks. 
Subtomogram averaging, CTF refinement and Bayesian polishing (previously 
called frame alignment) are as they were in in RELION-4.0, but the use 
of 2D particle stacks considerably speeds up initial model generation, 
3D classification and 3D refinement.

We hope that our definition of STAR files, with metadata required for 
and generated by our pipeline, will contribute to ongoing efforts in 
standardisation of the field. The upcoming CCP-EM tomography pipeline 
will be based around the same definitions.

A preprint describing the pipeline is here: 
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.04.26.591129v1__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4xyVf7rI$ 

A detailed tutorial, including precalculated results, is here: 
https://urldefense.com/v3/__https://relion.readthedocs.io/en/release-5.0/STA_tutorial/Introduction.html__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4KDyDYDk$ 

RELION-5.0 remains proudly open-source, and is completely free for all 
users. Download the code from: 
https://urldefense.com/v3/__https://github.com/3dem/relion/tree/ver5.0__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4S60FB6g$  and make sure you are using 
version RELION-5.0-beta-3 or newer, as several important bugs have 
recently been fixed.

Happy processing,

The RELION team (https://urldefense.com/v3/__https://relion.readthedocs.io/en/release-5.0/Team.html__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN44SfYOBQ$ )

-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
https://urldefense.com/v3/__http://www2.mrc-lmb.cam.ac.uk/groups/scheres__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4T0FrRJM$