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Outer-Boundary Assisted Segmentation and Quantification of Trabecular Bones by an Imagej Plugin
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BoneJ2 - refactoring established research software.

Richard Domander1, Alessandro A Felder1,2, Michael Doube1,3

  • 1Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, NW1 0TU, UK.

Wellcome Open Research
|May 14, 2021
PubMed
Summary
This summary is machine-generated.

Researchers improved BoneJ, skeletal biology image analysis software, by adopting modern programming practices. This reimplementation enhances software longevity and reusability for future scientific discovery.

Keywords:
BiologyBoneBoneJFIJIImage analysisImageJJavaMorphometryOpen-sourceProgrammingSoftware engineering

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Area of Science:

  • Scientific computing
  • Bioinformatics
  • Image analysis

Background:

  • Research software development often prioritizes rapid results over long-term code quality.
  • Expediently developed software may lack the flexibility and longevity required for sustained scientific use.
  • Skeletal biology image analysis software like BoneJ faces risks of becoming obsolete due to design limitations.

Purpose of the Study:

  • To address design limitations in BoneJ that threatened its usability.
  • To enhance the longevity, flexibility, and reusability of skeletal biology image analysis software.
  • To improve the overall quality and maintainability of the BoneJ codebase.

Main Methods:

  • Reimplementation of the BoneJ software for skeletal biology image analysis.
  • Adoption of contemporary programming best practices, including separation of concerns and dependency management.
  • Integration of thorough testing, continuous integration and deployment, and comprehensive documentation.

Main Results:

  • The reimplemented software, BoneJ2, demonstrates a significant improvement in code quality.
  • BoneJ2 incorporates modern development technologies and practices, enhancing its robustness.
  • The new version seamlessly integrates with the ImageJ2 plugin ecosystem, expanding its utility.

Conclusions:

  • Adopting contemporary programming practices is crucial for creating sustainable and reusable research software.
  • The enhanced BoneJ2 software provides a more reliable and adaptable tool for skeletal biology image analysis.
  • This work highlights a generational shift in developing research software, prioritizing quality and long-term value.