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<!DOCTYPE html>
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<title>ORMIR - Why a community</title>
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<li class="dropdown"><a href="#"><span>About us</span> <i class="bi bi-chevron-down"></i></a>
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<li><a href="motivation.html">Why a community</a></li>
<li><a href="members.html">Who we are</a></li>
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<h2>Why a community</h2>
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Get to know about our research, the challenges we aim to address, how we built a community to find solutions, and how we are organized!
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<h4><span>Our research<h4><span>
</div>
<p>
As musculoskeletal (MSK) imaging scientists, we extract <b>quantitative information from medical images</b> of bones, muscles, and joints to <b>investigate diseases</b> such as osteoporosis, osteoarthritis, and muscular dystrophies
</p>
<p>
Our approach involve workflows with a <strong>common structure</strong>, including:
<ul class="custom-list-tight">
<li class="custom-list-tight">
<strong> Acquisition of medical images </strong> using magnetic resonance or computed tomography
</li>
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<strong> Segmentation</strong> (i.e. labeling) of images to extract the organs of interest
</li>
<li>
<strong> Quantification</strong> of organ or tissue morphology, structure (e.g. cartilage thickness), chemical composition (e.g. calcium content), and mechanical response (e.g. strains and stresses)
</li>
</ul>
</p>
<p>
Our ultimate <b>goal</b> is to <b>create computational tools</b> to investigate diseases in a <b>reliable and robust</b> way
</p>
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<img src="assets/img/general/pipeline.png" class="img-fluid" alt="">
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<div class="section-sub-title">
<h4><span>Our challenges<h4><span></span>
</div>
<p> The <b>computational tools in our labs</b> are traditionally composed of <b>fragmented code</b>, resulting from a combination of proprietary software, in-house implementations, and occasionally open-source code. This approach presents several challenges:
<ul class="custom-list-tight">
<li>
When using <b>proprietary software</b>, it is <b>impossible to verify and modify parameters and implementations</b>, limiting our <b>awareness</b> of implementations and ability to <b>adapt</b> the code for new image modalities or anatomies
</li>
<li>
The life of <b>in-house code</b> is often <b>tied to the employment</b> of the code creators (mainly MSc students, PhD students, or PostDocs), restricting <b>code reuse and expansion</b> by newer lab members
</li>
<li>
Existing <b>open source software</b> is often difficult to reuse because of <b>insufficient documentation</b> and variability of programming languages
</li>
</ul>
</p>
<p>
To overcome these challenges, we <b>established the ORMIR community</b>. Our goal is to <b>develop open, reproducible, well-tested, and well-documented software to analyze musculoskeletal (MSK) images</b>
</p>
</div>
<hr>
<br>
<br>
<br>
<br>
<div class="col-md-12 offset-md-0">
<div class="section-sub-title">
<h4><span>How we started building a community<h4><span></span>
</div>
<p>
The <b>ideas of code sharing, openness, and reproducibility</b> as a solution to code fragmentation <b>began circulating</b> in our scientific community during <b>two satellite events</b> of the <a href="https://www.qmski.org/">Quantitative Musculoskeletal Imaging (QMSKI) Workshop</a> in 2019:
<i>Hands-on Transparent QMSKI research: Open data, reproducible workflows, and interactive publications</i>, and
<i>Working group on standardization of quantitative metrics for 3D imaging</i>
</p>
<p>
A few months later, a group of researchers <b>successfully applied</b> for funds to hold a <b>Jupyter Community Workshop</b> entitled <a href="https://github.com/JCMSK/2022_JCW/blob/main/README.md">Building the Jupyter Community in MSK Imaging Research</a>. We consider the day of acceptance of the proposal, 24 January 2020, as the birthdate of our community. You can read more about our beginnings in our <a href="https://zenodo.org/doi/10.5281/zenodo.8119062">manifesto paper</a>
</p>
<p>
Since 2020, we have <b>grown</b> to include more and more <a href="members.html">MSK researchers and contributors from academia and industry</a>. We have developed <a href="software.html">Python packages</a>, written <a href="publications.html">publications</a>, applied for <a href="funding.html">funds</a>, and hosted <a href="events.html">workshops</a>
</p>
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<br>
<div class="col-md-12 offset-md-0">
<div class="section-sub-title">
<h4><span>How we are organized<h4><span></span>
</div>
<p>We are divided in <a href="groups.html">working groups</a>, based on our <b>research interests</b>. Each working group has one or more <b>coordinators</b> that support <b>contributors</b> in finding their way to participate in projects
</p>
<p>We also have a <a href="boards.html#CAB">Community Advisory Board</a> and a <a href="boards.html#TAB">Technical Advisory Board</a>, who <b>coordinate the community outreach</b> and <b>provide technical support</b>
</p>
<p>We share common <a href="index.html#goals">goals</a> and <a href="index.html#values">values</a> and we are <b>always open to welcoming</b> <a href="newcomers.html">new contributors</a>
</p>
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<strong>We promote open and reproducible research</strong> with workshops and talks.
See the <a href="https://github.com/JCMSK/2022_JCW/blob/main/README.md#numfocus-blog-post">report</a> of our latest workshop
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