Strain Analysis Software for Open Science

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PROJECT SUMMARY The parent grant focuses on interfaces between tissues either transfer load (requiring toughness) or provide a smooth surface (requiring low friction). Fibrous interfaces are very effective at transferring load between tissues, e.g., at connective tissue-bone interfaces (“entheses”), peritoneal-mesentery interfaces, interfaces between layers of the vasculature, and the pia mater. These interfaces require toughness to resist high stresses associated with material mismatches. Surgical repair can lead to smooth interfaces becoming fibrous, (e.g., following hernia surgery) or to tough interfaces becoming weak (e.g., following tendon- and ligament-to- bone repair). In older patients with large rotator cuff repairs, for example, where the desired attachment is not reformed, up to 94% of surgical repairs fail. These challenges arise in part because the features that endow fibrous interfaces with toughness are not known. The parent grant there for aims to develop a comprehensive modeling and experimental approach for studying the factors underlying the transition from tough to weak in a fibrous interface. The supplement proposes to take software that we have developed in the course of this work and make it cloud-ready and broadly available. This software enables quantitative analysis of deformation in microscopy and medical imaging. Although commercial software for this is widespread, these packages employ regularization techniques to ensure a smooth solution, and are therefore often unable to accurately identify local tissue deformations or predict soft tissue tears. We will enable research into the relation between strain fields, injury, and rehabilitation by executing two aims. (1) We will develop open-source, user-friendly software as a plugin to ImageJ for the strain-tracking algorithm in two dimensions (2D), stereo view (2.5D), and three dimensions (3D). Best practices will be used for open source software development, and modules will be created to facilitate the development of a user community. (2) We will develop a working, static code implementation on GitHub that can be run on Amazon AWS using data in the cloud. This will help overcome the second obstacle to widespread adoption of strain mapping techniques in musculoskeletal research, namely that the 3D datasets that must be acquired require substantial computational resources to analyze. The work will enable collaboration between the PIs of the parent grant and an expert on open source software development for clinical and research translation, and enhance the impact of a tool with strong potential.