# Strain Analysis Software for Open Science

> **NIH NIH R01** · WASHINGTON UNIVERSITY · 2021 · $210,057

## Abstract

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.

## Key facts

- **NIH application ID:** 10406113
- **Project number:** 3R01AR077793-02S1
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Guy M Genin
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $210,057
- **Award type:** 3
- **Project period:** 2020-09-01 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10406113

## Citation

> US National Institutes of Health, RePORTER application 10406113, Strain Analysis Software for Open Science (3R01AR077793-02S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10406113. Licensed CC0.

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