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
What do we do?¶
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
Italy
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.