[paper reading] tomoalign: a novel approach to correcting sample motion and 3D CTF in cryoet

essential information

author ：Jose Jesus Fernandez（ A research institute in Spain ）, Sam Li （ University of California ）
Periodical ：Journal of Structural Biology, 2021
Source code: None

Abstract

TomoAlign It's a software package , Some tools are integrated to alleviate two important resolution constraints in tomography ：
1. Sample motion caused by electron beam
2. Contrast transfer function of microscope （CTF)

• The software pays special attention to Thick sample Tomography of , they Benchmark markers are required For accurate tilt sequence registration and sample motion estimation .
• The electron beam induced... Experienced during tilt sequence acquisition is established Sample motion model , The motion model can be used to generate sub tilt sequences of motion correction centered on the particles of interest .
• Besides , It determines on each tilted image Each particle Defocus and correct , Thus, motion correction and CTF Corrected sub tilt sequence （subtilt-series）. Or it can put CTF The message goes out , And then in RELION Wait for the external package to execute CTF correct .
• TomoAlign As a multifunctional tool , In the process of determining the in-situ structure , Simplify the initial alignment of the tilt sequence to the average of the final sub faults cryoET Workflow .

Conclusion

Method

TomoAlign technological process ：（3 steps）

1. The slant sequence registration based on markers is realized , It includes the estimation of sample motion , obtain Motion models .
2. Then the motion model can be used Fault reconstruction , Generate motion compensated tomography . In order to reduce computing time and disk occupation , This fault reconstruction is usually calculated within the box size （ Usually 4x, 6x）, And don't think about CTF correct . Then the particles of interest are selected and their coordinates recorded .
3. Once the particles of interest are identified , The last step is Extract the relevant subtilt Sequence . Use the motion model determined in the first step to provide motion compensation subtilt Sequence . Besides , About each tilt Of CTF Information allows it to find out based on coordinates and acquisition geometry One by one for each particle tilt Of CTF, With Generate CTF Corrective subtilt Sequence . perhaps , He will record in the data file 3D-CTF Information , And no CTF Corrected subtilt The sequence is provided to other software packages . Then use an external program to output subtilt Sequence for fault reconstruction , Tomographic image of afterbirth progeny , For subsequent sub sectional image averaging .

TomoAlign Direct sum IMOD docking , from IMOD Receive marker models and tilt-series, In raw or aligned stack form , use MRC File format . The reconstructed sectional image adopts MRC Format . For the last step , You can use any common software to provide particle coordinates and each tilt Defocus value of .

TomoAlign You can talk to Relion docking , With MRC Format write output subtilt Sequence and contain star Format alignment and CTF Metadata file of parameters . Sub fault map reconstruction is best used Relion The inverse Fourier transform of , You can also use other , such as Tomo3D Weighted back projection algorithm （WBP）. After exercise correction 、CTF The corrected sub fault map can be used as the input of other sub fault averaging software .

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$$Author：Chier$$