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Subtomogram Averaging

This website hosts tutorials for subtomogram averaging using TOMOMAN and STOPGAP.

Workflow

We will disucss data preprocessing, tomogram reconstruction, and subtomogram averaging using our TOMOMAN/STOPGAP pipeline. A typical cryo-electron tomography (cryo-ET) workflow is illustrated below.

workflow

TOMOMAN

TOMOMAN, i.e. TOMOgram MANager, is a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms. TOMOMAN mainly acts as a set of wrapper scripts for external packages, managing the input and outputs of each external module to form a cohesive pipeline. Preprocessing metadata is collected into the TOMOMAN "tomolist" (default name tomolist.mat) while output is written to a plain-text log file (default name: tomoman.log). For more information about TOMOMAN, see Khavnekar & Wan. bioRxiv. 2024.

STOPGAP

STOPGAP is a real-space correlation-based package for template matching, subtomogram alignment and averaging, and classification. STOPGAP's main goal is to provide users a set of useful subtomogram averaging algorithms while making virtually all parameters readily accesible. This is based around the notion that every biological problem has unqiue requirements on cryo-ET, and that the user is best suited to determining these requirements. It is an open-source package written in MATLAB, and is primarily designed to run on CPUs in high-performance computing (HPC) environments. For more information about STOPGAP, see Wan et al. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2024.

Courses

Previous workshops using this tutorial: