Document Type

Article

Publication Date

2023

DOI

10.3390/ijms242417183

Publication Title

International Journal of Molecular Sciences

Volume

24

Issue

24

Pages

17183 (1-15)

Abstract

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating from the seed points form short linear candidate filament segments, which are further scrutinized and classified by users via inspection of a novel pruning map, which visualizes the likelihood of being a part of longer filaments. The pruned linear candidate filament segments are then iteratively fused into continuous, longer, and curved filaments based on their relative orientations, gap spacings, and extendibility. When applied to the simulated phantom tomograms of a Dictyostelium discoideum filopodium under experimental conditions, Struwwel Tracer demonstrated high efficacy, with F1-scores ranging from 0.85 to 0.90, depending on the noise level. Furthermore, when applied to a previously untraced experimental tomogram of mouse fibroblast lamellipodia, the filaments predicted by Struwwel Tracer exhibited a good visual agreement with the experimental map. The Struwwel Tracer framework is highly time efficient and can complete the tracing process in just a few minutes. The source code is publicly available with version 3.2 of the free and open-source Situs software package.

Rights

© 2023 The Authors.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY 4.0) License.

Data Availability

Article states: "The source of Struwwel Tracer can be freely downloaded at https://situs.biomachina.org in Situs version 3.2."

Original Publication Citation

Sazzed, S., Scheible, P., He, J., & Wriggers, W. (2023). Untangling irregular actin cytoskeleton architectures in tomograms of the cell with Struwwel Tracer. International Journal of Molecular Sciences, 24, 1-15, Article 17183. https://doi.org/10.3390/ijms242417183

ORCID

0000-0002-8552-5337 (Sazzed), 0000-0001-5326-3152 (Wriggers)

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