ORMIR - Publications

Publications

Here are our preprints, journal papers, and conference abstracts

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.
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.

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.
Crimi G, Vanella N, Schileo E, Valente G, Fraterrigo G, Taddei F
ALBA: Agile library for biomedical applications
2025. SoftwareX, 31, 102188.
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.
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.
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.

MT Kuczynski, NJ Neeteson, KS Stok, AJ Burghardt, MAE Espinosa, J Vicory, JJ Tse, P Durongbhan, S Bonaretti, AKO Wong, SK Boyd, DE Whittier, SL Manske
Measuring trabecular thickness and separation from HR-pQCT using the ORMIR_XCT package
3-8 November 2024. 24th International Workshop on Quantitative Musculoskeletal Imaging. The Barossa Valley, Australia.
S Bonaretti, MAE Hernandez, F Chiumento, Y Founas, M Froeling, J Hirvasniemi, G Iori, Y Lee, S Matuschik, M Monzon, F Santini, D Cameron
ORMIR-MIDS: An open standard for curating and sharing musculoskeletal imaging data
3-8 November 2024. 24th International Workshop on Quantitative Musculoskeletal Imaging. The Barossa Valley, Australia.
G Fraterrigo, AD Santamaria, M Pani, G Crimi, F Taddei, E Schileo, G Iori
Open trabecular bone microFE models from microCT images: Ciclope new release with higher performances and verified tetra mesh option
3-8 November 2024. 24th International Workshop on Quantitative Musculoskeletal Imaging. The Barossa Valley, Australia.

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