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A roadmap to reconstructing muscle architecture from CT data


Katzke, Julian; Puchenkov, Pavel; Economo, Evan P.; Stark, Heiko (2022), A roadmap to reconstructing muscle architecture from CT data, Dryad, Dataset,


Skeletal muscle is responsible for voluntary force generation across animals, and muscle architecture largely determines the parameters of mechanical output. The ability to analyze muscle performance through muscle architecture is thus a key step towards better understanding the ecology and evolution of movements and morphologies. In pennate skeletal muscle, volume, fiber lengths and attachment angles to force transmitting structures comprise the most relevant parameters of muscle architecture. Measuring these features through tomographic techniques offers an alternative to tedious and destructive dissections, particularly as the availability of tomographic data is rapidly increasing.  However, there is a need for streamlined computational methods to access this information efficiently. Here, we establish and compare workflows using partially automated image analysis for fast and accurate estimation of animal muscle architecture. After isolating a target muscle through segmentation, we evaluate freely available and proprietary fiber tracing algorithms to reconstruct muscle fibers. We then present a script using the Blender Python API to estimate attachment angles, fiber lengths, muscle volume and Physiological Cross-Sectional Area. We apply these methods to insect and vertebrate muscle and provide guided workflows. Results from fiber tracing are consistent compared to manual measurements but much less time-consuming. Lastly, we emphasize the capabilities of the open-source 3D software Blender as both a tool for visualization and a scriptable analytic tool to process digitized anatomical data. Across organisms, it is feasible to extract, analyze, and visualize muscle architecture from tomography data by exploiting the spatial features of scans and the geometric properties of muscle fibers. As digital libraries of anatomies continue to grow, the workflows and approach presented here can be part of the open-source future of digital comparative analysis. 

Usage Notes

Please refer to the ReadMe on what individual files are and what they're for.

Data is structured into full ant dataset, resampled ant dataset, bird dataset in separate .zip folders