WikiSysop: Created page with "== Citation == S. Sazzed, P. Scheible, J. He, and W. Wriggers, “Untangling irregular actin cytoskeleton architectures in tomograms of the cell with struwwel tracer,” Intl. J. Molecular Sciences, vol. 24, no. 24, p. 17183, 2023. == 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 intracellu..."

2024-10-18T06:52:32Z

Created page with "== Citation == S. Sazzed, P. Scheible, J. He, and W. Wriggers, “Untangling irregular actin cytoskeleton architectures in tomograms of the cell with struwwel tracer,” Intl. J. Molecular Sciences, vol. 24, no. 24, p. 17183, 2023. == 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 intracellu..."

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== Citation ==

S. Sazzed, P. Scheible, J. He, and W. Wriggers, “Untangling irregular actin cytoskeleton architectures in tomograms of the cell with struwwel tracer,” Intl. J. Molecular Sciences, vol. 24, no. 24, p. 17183, 2023.

== 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.

== Keywords ==

== Links ==

https://www.mdpi.com/1422-0067/24/24/17183

== Related software ==

== Related methods ==

== Comments ==

2023Sazzed Struwwel - Revision history