Publications
Preprints
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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
Open and reproducible research in musculoskeletal imaging: Why it matters and how to implement it with the guidelines of the ORMIR community
3 October 2025.
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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
Introducing the Open and Reproducible Musculoskeletal Imaging Research (ORMIR) community
6 July 2023.
Journal papers
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Ritsche P, Sarto F, Santini F, Leitner C, Franchi M, Faude O, Finni T, Seynnes O, Cronin N
UMUD: a web application for easy access to musculoskeletal ultrasonography datasets
2026.
BMC Med Imaging.
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Santini F, Monzon M, Poncioni S, Bonaretti S, Hirvasniemi J, Froeling M, Cameron D
ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data
2026.
JBMR Plus 2026:ziag013.
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Walle M , BE Matheson BE, Boyd SK
Comparing linear and nonlinear finite element models of vertebral strength across the thoracolumbar spine: a benchmark from density-calibrated computed tomography
2025.
GigaScience, Volume 14, 2025, giaf094.
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Crimi G, Vanella N, Schileo E, Valente G, Fraterrigo G, Taddei F
ALBA: Agile library for biomedical applications
2025.
SoftwareX, 31, 102188.
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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
ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing
2024.
Journal of Open Source Software, 9(97), 6084.
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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
Deep Anatomical Federated Network (Dafne): an open client/server framework for the continuous collaborative improvement of deep-learning-based medical image segmentation
2023.
Preprint.
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Iori G, Crimi G, Schileo E, Taddei F, Fraterrigo G, Pani M
Ciclope: micro Computed Tomography to Finite Elements
2023.
Journal of Open Source Software, 8(84), 4952.
Conference abstracts
- Ritsche P, Santini F, Bonaretti S, Cameron D, Faude O
Implementing Open and Standardized Data Practices in Musculoskeletal Imaging: ORMIR and UMUD
17th Annual Conference of the Swiss Society of Sport Science.
11-12 February 2026.
Fribourg, Switzerland
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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
ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data
41st Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB).
8-11 October 2025.
Marseille, France
🏆 "MRI Together" Open Science Award (2nd place) 🏆
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Visani V, Veronese M, Tamanti A, Pizzini FB, Calabrese M, Castellaro M, Santini F
Assessing Generalizability in Choroid Plexus Automatic Segmentation: A Comparison of ASCHOPLEX Fine-Tuning and Dafne Federated Incremental Learning
41st Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB).
8-11 October 2025.
Marseille, France
🏆 "MRI Together" Open Science Award (3rd place) 🏆
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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
Measuring trabecular thickness and separation from HR-pQCT using the ORMIR_XCT package
24th International Workshop on Quantitative Musculoskeletal Imaging.
3-8 November 2024.
The Barossa Valley, Australia.
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Bonaretti S, Hernandez MAE, Chiumento F, Founas Y, Froeling M, Hirvasniemi J, Iori G, Lee Y, Matuschik S, Monzon M, Santini F, Cameron D
ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data
24th International Workshop on Quantitative Musculoskeletal Imaging.
3-8 November 2024.
The Barossa Valley, Australia.
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Fraterrigo G, Santamaria AD, Pani M, Crimi G, Taddei F, Schileo E, Iori G
Open trabecular bone microFE models from microCT images: Ciclope new release with higher performances and verified tetra mesh option
24th International Workshop on Quantitative Musculoskeletal Imaging.
3-8 November 2024.
The Barossa Valley, Australia.
🏆 Winner of the Open Science Award 🏆
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