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<!DOCTYPE html>
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<title>ORMIR - Publications</title>
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<h2>Publications</h2>
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<div class="section-sub-title">
Here are our <a href="#preprints">preprints</a>, <a href="#papers">journal papers</a>, and <a href="#abstracts">conference abstracts</a>
</div>
<br>
<br>
<!---------- PREPRINTS ---------->
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<span class="anchor" id="preprints"></span>
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<h3>Preprints</h3>
</p>
<ul class="custom-list">
<li>
Bonaretti S, Barzaghi L, Barzegari M, Burghardt A, Cameron D, Carballido-Gamio J, Crimi G, Durongbhan P, Espinosa Hernandez M, Fraterrigo G, Grassi L, Greer H, Iori G, Kuczynski M, Manske S, McCormick M, Neeteson N, Niethammer M, Pani M, Quintiens J, Sadeghi M, Santini F, Schileo E, Stok K, Taddei F, Tse J, Vicory J, Wesseling M, Wong A, Zukić D
<br>
<a href="https://doi.org/10.5281/zenodo.8119062">
<strong>Introducing the Open and Reproducible Musculoskeletal Imaging Research (ORMIR) community</strong>
</a>
<br>
6 July 2023.
</li>
</ul>
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<br>
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<br>
<br>
<!---------- JOURNAL PAPERS ---------->
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<div class="col-md-12 offset-md-0">
<!-- Trick to jump at the top of the title (not bottom) for internal links -->
<span class="anchor" id="papers"></span>
<p>
<h3>Journal papers</h3>
</p>
<ul class="custom-list">
<li>
Bonaretti S, Barzegari M, Bevers M, Boyd S, Burghardt AJ, Cameron D, Chiumento F, Crimi G, Degenhart G, Durongbhan P, Espinosa Hernandez MA, Fraterrigo G, Ghasem-Zadeh A, Grassi L, Hirvasniemi J, Hosseinitabatabaei M, Iori G, Kok J, Kuczynski M, Lee Y, Liberati C, Manske S, McCormick M, Monzon M, Pani M, Poncioni S, Quintiens J, Räuber S, Ritsche P, Santamaria A, Santini F, Sarto F, Schileo E, Stadelmann V, Stok KS, Surowiec R, Taddei F, Vicory J, Walle M, Wesseling M, Whittier D, Willie B, Wong AKO, Zukić D
<br>
<a href="https://doi.org/10.1093/jbmrpl/ziag025">
<strong>Open and reproducible research in musculoskeletal imaging: Why it matters and how to implement it with the guidelines of the ORMIR community</strong>
</a>
<br>
2026.
JBMR Plus 2026, ziag015.
</li>
<li>
Ritsche P, Sarto F, Santini F, Leitner C, Franchi M, Faude O, Finni T, Seynnes O, Cronin N
<br>
<a href="https://doi.org/10.1186/s12880-026-02170-0">
<strong>UMUD: a web application for easy access to musculoskeletal ultrasonography datasets</strong>
</a>
<br>
2026.
BMC Med Imaging.
<br>
<!-- GitHub -->
<a href="https://github.com/PaulRitsche/UMUD/" alt = "GitHub repository"><i class="bi bi-github"></i></a>
</li>
<li>
Santini F, Monzon M, Poncioni S, Bonaretti S, Hirvasniemi J, Froeling M, Cameron D
<br>
<a href="https://doi.org/10.1093/jbmrpl/ziag013">
<strong>ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data</strong>
</a>
<br>
2026.
JBMR Plus 2026, ziag013.
<br>
<!-- GitHub -->
<a href="https://github.com/ormir-mids/ormir-mids" alt = "GitHub repository"><i class="bi bi-github"></i></a>
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</li>
<li>
Walle M , BE Matheson BE, Boyd SK
<br>
<a href="https://doi.org/10.1093/gigascience/giaf094">
<strong>Comparing linear and nonlinear finite element models of vertebral strength across the thoracolumbar spine: a benchmark from density-calibrated computed tomography</strong>
</a>
<br>
2025.
GigaScience, Volume 14, 2025, giaf094.
<br>
<!-- GitHub -->
<a href="https://github.com/Bonelab/spineFE-benchmark" alt = "GitHub repository"><i class="bi bi-github"></i></a>
<!-- Dataset -->
<a href="https://gigadb.org/dataset/102733"><i class="bi bi-database-fill"></i></a>
</li>
<li>
Crimi G, Vanella N, Schileo E, Valente G, Fraterrigo G, Taddei F
<br>
<a href="https://doi.org/10.1016/j.softx.2025.102188">
<strong>ALBA: Agile library for biomedical applications</strong>
</a>
<br>
2025.
SoftwareX, 31, 102188.
<br>
<!-- GitHub -->
<a href="https://github.com/IOR-BIC/ALBA" alt = "GitHub repository"><i class="bi bi-github"></i></a>
</li>
<li>
Kuczynski MT, Neeteson NJ, Stok KS, Burghardt AJ, Espinosa Hernandez MA, Vicory J, Tse JJ, Durongbhan P, Bonaretti S, Wong AKO, Boyd SK, Manske SL
<br>
<a href="https://doi.org/10.21105/joss.06084">
<strong>ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing</strong>
</a>
<br>
2024.
Journal of Open Source Software, 9(97), 6084.
<br>
<!-- GitHub -->
<a href="https://github.com/ORMIR-XCT"><i class="bi bi-github"></i></a>
<!-- Demo data -->
<a href="https://github.com/SpectraCollab/ORMIR_XCT/tree/main/examples/images"><i class="bi bi-database-fill"></i></a>
</li>
<li>
Santini F, Wasserthal J, Agosti A, Deligianni X, Keene KR, Kan HE, Sommer S, Stuprich C, Wang F, Weidensteiner C, Manco G, Paoletti M, Mazzoli V, Desai A, Pichiecchio A
<br>
<a href="https://doi.org/10.48550/arXiv.2302.06352">
<strong>Deep Anatomical Federated Network (Dafne): an open client/server framework for the continuous collaborative improvement of deep-learning-based medical image segmentation</strong>
</a>
<br>
2023.
Preprint.
<br>
<!-- GitHub -->
<a href="https://github.com/dafne-imaging"><i class="bi bi-github"></i></a>
</li>
<li>
Iori G, Crimi G, Schileo E, Taddei F, Fraterrigo G, Pani M
<br>
<a href="https://www.doi.org/10.21105/joss.04952">
<strong>Ciclope: micro Computed Tomography to Finite Elements</strong>
</a>
<br>
2023.
Journal of Open Source Software, 8(84), 4952.
<br>
<!-- GitHub -->
<a href="https://github.com/gianthk/ciclope" alt = "GitHub repository"><i class="bi bi-github"></i></a>
<!-- Demo data -->
<a href="https://github.com/gianthk/ciclope/tree/master/test_data"><i class="bi bi-database-fill"></i></a>
</li>
</ul>
</div>
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</div>
<br>
<br>
<hr>
<br>
<br>
<!---------- CONFERENCE ABSTRACTS ---------->
<div class="row">
<div class="col-md-12 offset-md-0">
<!-- Trick to jump at the top of the title (not bottom) for internal links -->
<span class="anchor" id="abstracts"></span>
<p>
<h3>Conference abstracts</h3>
</p>
<ul class="custom-list">
<li>Ritsche P, Santini F, Bonaretti S, Cameron D, Faude O
<br>
<a href="https://doi.org/10.36950/2026.2ciss059">
<strong>Implementing Open and Standardized Data Practices in Musculoskeletal Imaging: ORMIR and UMUD</strong>
</a>
<br>
17th Annual Conference of the Swiss Society of Sport Science.
11-12 February 2026.
Fribourg, Switzerland
</li>
<li>
Santini F, Bonaretti S, Espinosa Hernandez MA, Chiumento F, Founas Y, Froeling M, Hirvasniemi J, Iori G, Lee Y, Räuber S, Monzon M, Poncioni S, Scharff Poulsen N, Walter G, Cameron D
<br>
<a href="https://www.springermedicine.com/book-of-abstracts-esmrmb-2025-online-41st-annual-scientific-meet/51726282">
<strong>ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data</strong>
</a>
<br>
41st Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB).
8-11 October 2025.
Marseille, France
<br>
🏆 "MRI Together" Open Science Award (2nd place) 🏆
</li>
<li>
Visani V, Veronese M, Tamanti A, Pizzini FB, Calabrese M, Castellaro M, Santini F
<br>
<a href="https://www.springermedicine.com/book-of-abstracts-esmrmb-2025-online-41st-annual-scientific-meet/51726282">
<strong>Assessing Generalizability in Choroid Plexus Automatic Segmentation: A Comparison of ASCHOPLEX Fine-Tuning and Dafne Federated Incremental Learning</strong>
</a>
<br>
41st Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB).
8-11 October 2025.
Marseille, France
<br>
🏆 "MRI Together" Open Science Award (3rd place) 🏆
</li>
<li>
Kuczynski MT, Neeteson NJ, Stok KS, Burghardt AJ, Espinosa MAE, Vicory J, Tse JJ, Durongbhan P, Bonaretti S, Wong AKO, Boyd SK, Whittier DE, Manske SL
<br>
<a href="https://doi.org/10.1093/jbmrpl/ziaf035">
<strong>Measuring trabecular thickness and separation from HR-pQCT using the ORMIR_XCT package</strong>
</a>
<br>
24th International Workshop on Quantitative Musculoskeletal Imaging.
3-8 November 2024.
The Barossa Valley, Australia.
</li>
<li>
Bonaretti S, Hernandez MAE, Chiumento F, Founas Y, Froeling M, Hirvasniemi J, Iori G, Lee Y, Matuschik S, Monzon M, Santini F, Cameron D
<br>
<a href="https://doi.org/10.1093/jbmrpl/ziaf035">
<strong>ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data</strong>
</a>
<br>
24th International Workshop on Quantitative Musculoskeletal Imaging.
3-8 November 2024.
The Barossa Valley, Australia.
</li>
<li>
Fraterrigo G, Santamaria AD, Pani M, Crimi G, Taddei F, Schileo E, Iori G
<br>
<a href="https://doi.org/10.1093/jbmrpl/ziaf035">
<strong>Open trabecular bone microFE models from microCT images: Ciclope new release with higher performances and verified tetra mesh option</strong>
</a>
<br>
24th International Workshop on Quantitative Musculoskeletal Imaging.
3-8 November 2024.
The Barossa Valley, Australia.
<br>
🏆 Winner of the Open Science Award 🏆
</li>
</ul>
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