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Introduction to The Musculoskeletal Atlas Project (MAP)

Posted on June 20, 2016

Subject-specific computational models of the musculoskeletal system have tremendous potential for clinical and sporting applications. A common approach to generate musculoskeletal models is to scale a generic model to match subject-specific landmarks, which are typically taken from optical motion capture. However, simple linear scaling does not account for individual variation in bone geometry and inaccurate landmark identification can result in non-physiological segment lengths. Furthermore, joint centres and joint axes in scaled generic models are often not adjusted to match an individual subject. Another approach is to generate subject-specific models from medical imaging data, although this process is time-consuming, costly, and requires a high level of expertise involving specialised software.

Data reduction methods, such as Principal Component Analysis, or PCA, can be used to efficiently characterise the morphological variation of bones across a population, sometimes referred to as a ‘shape model’. Shape models have excellent potential to assist in the generation of subject-specific musculoskeletal models. Our research group at the Auckland Bioengineering Institute has developed an open-source software platform, called the Musculoskeletal Atlas Project (MAP), to enable biomechanics researchers to rapidly generate musculoskeletal models using population-based scaling (see the following webinar on customising OpenSim models). The main advantage of using a shape model to perform geometric scaling is that the resulting musculoskeletal model is constrained by an underlying model of physiological anatomy and the joint centres and axes can easily be re-calculated and embedded into the model. The surface geometry output from the MAP Client can be used with various software platforms for simulation, such as OpenSim, FEBio, OpenCMISS, etc (see Figure).

Overview of the Musculoskeletal Atlas Project. The MAP Client receives input and provides an interface to an underlying database and model repository. Output from the MAP Client includes models compatible with other simulation software.

Overview of the Musculoskeletal Atlas Project. The MAP Client receives input and provides an interface to an underlying database and model repository. Output from the MAP Client includes models compatible with other simulation software.

The MAP platform is based around a workflow manager, called the MAP Client, which is a cross-platform application that can be used to create workflows from a collection of workflow steps. Each workflow step is simply a plugin, which performs tasks of varying complexity (e.g. segmentation, mesh fitting, registration, PCA-based fitting, etc). The entire code base is written in Python to enable easy sharing. Indeed, the central idea for the MAP Client is to allow users to develop and share their own plugins that can be used in a workflow. The requirements for developing a workflow step have been kept as low as practicable thus allowing plugin creators to concentrate on the practical implementation of the step rather than conforming to the plugin API. Additionally the Plugin Wizard tool greatly simplifies the first stage in creating a workflow step and generates a considerable amount of the skeleton code required. You can learn more about MAP by browsing the documentation at https://map-client.readthedocs.io/en/latest/ or by downloading the code from GitHub: https://github.com/MusculoskeletalAtlasProject/mapclient

Having a plugin based framework makes it possible for groups to share their workflows and workflow steps without requiring a lot of extraneous software. Also having users create and share their plugins increases the flexibility of the MAP Client and distances users from relying on an external team of developers. Imagine an active ISB community of MAP Client users that can share their code, experience, and ideas. Perhaps organized sessions and workshops at the next ISB conference to learn about new methods and share workflows?

Please get in touch to let us know what you think, if you are interested to learn more about the Musculoskeletal Atlas Project, and would like to contribute or get started.

 

Thor Besier  (t.besier@auckland.ac.nz)

Informatics Officer, ISB

Auckland Bioengineering Institute and Dept of Engineering Science, University of Auckland

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