Outlier Detection and Angular Constraining for
Subtomogram Alignment in cryoET
J.J. Fernandez (1,2), S. Li (3)
(1) Spanish National Research Council (CINN-CSIC). Oviedo. Spain.
(2) Health Research Institute of Asturias (ISPA). Oviedo. Spain.
(3) Dept. Biochemistry and Biophysics. UCSF. USA.
Contact: jjfernandez.software @ gmail.com
Description
RANSAC is a software program that analyzes the alignment parameters of subtomograms extracted from continuous filament-like structures (e.g. triplet microtubules in centrioles, doublet microtubules in axonemes, true filaments), detects potentially misaligned subtomograms and estimates their correct alignment from the neighbouring subtomograms by imposing an angular consistency constraint. To this end, the program uses the RANSAC method (RANdom SAmple Consensus) to model the alignment of the filament-related subtomograms and determine the subtomograms that are not consistent with the model (i.e. outliers). The alignment parameters of the outliers are then corrected based on the model calculated from the inliers. The program RANSAC accepts input alignment parameters in Spider/Xmipp format obtained with Xmipp MLTOMO and produces output in the same format. Future versions of the program will accept other formats on demand (e.g. Relion Star), just ask for it at the contact address.
If you use RANSAC in your works, please cite any of the following articles where this program has been used:
The structure of basal body inner junctions from Tetrahymena revealed by electron cryo-tomography.
S Li, JJ Fernandez, MD Ruehle, RA Howard-Till, A Fabritius, CG Pearson, DA Agard, ME Winey
EMBO Journal (in press), 2025
https://doi.org/10.1038/s44318-025-00392-6
Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila.
S Li, JJ Fernandez, AS Fabritius, DA Agard, M Winey
Life Science Alliance 5(3):e202101225, 2022.
https://doi.org/10.26508/lsa.202101225
Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism.
S Li, JJ Fernandez, WF Marshall, DA Agard
eLife 8:e43434, 2019.
https://doi.org/10.7554/elife.43434
Download the package
Current version: 1.0 (November 2024)
Available material:
Documentation in PDF: ransac.pdf
Binaries for x86-based platforms under Linux (64 bits) and Windows WSL.
Binaries for Macs based on Intel and Apple Silicon processors under OSX/macOS.
The development of RANSAC has been supported by the HHMI, NIH, Fundacion Ramon Areces and Spanish AEI/FEDER.
Copyright by the authors.