Motivation and Vision

Computational workflows in MSK imaging

In quantitative MSK imaging, we extract quantitative information from medical images of bones, muscles, and joints to investigate diseases such as osteoporosis and osteoarthritis.

Our computational workflows have a similar structure:

  • Acquisition of medical images using magnetic resonance or computed tomography
  • Segmentation (i.e. labeling) of images to extract the organ/s of interest
  • Computation of metrics to quantify organ or tissue morphology, structure (e.g. cartilage thickness), chemical composition (e.g. calcium content), and mechanical response (e.g. strains and stresses)

Our goal is to create computational tools to investigate diseases in a reliable and robust way

Why a community for open and reproducible research?

Although we share a similar workflow structures, we experience several challenges:

  • Created code is usually fragmented, as it mainly consists of a combination of proprietary software and in-house algorithms
  • When dealing with proprietary software, it is impossible to verify parameters and implementations and adapt the code to new images or anatomies
  • The life of in-house code is strictly linked to the employment of the code creators, restricting code reuse and expansion by newer lab members
  • In our research field, software is usually not open and, when open, it is often hard to reuse because of lack of documentation
To overcome these issues, we create the ORMIR community. Our main aim is to create open, reproducible, well-tested, and well-documented software to analyze musculoskeletal (MSK) images. To know more about our story, read the manifesto paper (coming soon!)

What do we do?

  • We write code! We create Python packages with Jupyter Notebooks as user-interface, focusing on application related to our research interest (see our packages)
  • We promote open and reproducible research with workshops and talks. See the report of our latest workshop

Who we are

We are a group of scientist in musculoskeletal imaging from academia and industry. Our aim is to create tools to make our research outputs open and reproducible.

Leonardo Barzaghi Mondino Foundation Pavia

Technical Advisory Board

Our role is to create tools and provide directions for code standardization and homogenization

Community Advisory Board

Our role is to coordinate community directions and outreach activities

Code of conduct

The ORMIR community is an engaged and respectful community composed of scientists from all over the world, who are committed to fostering a productive, professional, and inclusive environment for everyone. We have adopted the Code of Conduct of Project Jupyter. In a nutshell: be friendly, welcoming, considerate, and respectful.