MiceBoneChallenge: Micro-CT public dataset and six solutions for automatic growth plate detection in micro-CT mice bone scans

Nikolay Burlutskiy; Marija Kekic; Jordi de la Torre; Philipp Plewa; Mehdi Boroumand; Julia Jurkowska; Borjan Venovski; Maria Chiara Biagi; Yeman Brhane Hagos; Roksana Malinowska-Traczyk; Yibo Wang; Jacek Zalewski; Paula Sawczuk; Karlo Pintarić; Fariba Yousefi; Leif Hultin

arXiv · 2411.17260

MiceBoneChallenge: Micro-CT public dataset and six solutions for automatic growth plate detection in micro-CT mice bone scans

Nikolay Burlutskiy·Marija Kekic·Jordi de la Torre·Philipp Plewa·Mehdi Boroumand·Julia Jurkowska·Borjan Venovski·Maria Chiara Biagi·Yeman Brhane Hagos·Roksana Malinowska-Traczyk·Yibo Wang·Jacek Zalewski·Paula Sawczuk·Karlo Pintarić·Fariba Yousefi·Leif Hultin

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Abstract

Detecting and quantifying bone changes in micro-CT scans of rodents is a common task in preclinical drug development studies. However, this task is manual, time-consuming and subject to inter- and intra-observer variability. In 2024, Anonymous Company organized an internal challenge to develop models for automatic bone quantification. We prepared and annotated a high-quality dataset of 3D $\mu$CT bone scans from $83$ mice. The challenge attracted over $80$ AI scientists from around the globe who formed $23$ teams. The participants were tasked with developing a solution to identify the plane where the bone growth happens, which is essential for fully automatic segmentation of trabecular bone. As a result, six computer vision solutions were developed that can accurately identify the location of the growth plate plane. The solutions achieved the mean absolute error of $1.91\pm0.87$ planes from the ground truth on the test set, an accuracy level acceptable for practical use by a radiologist. The annotated 3D scans dataset along with the six solutions and source code, is being made public, providing researchers with opportunities to develop and benchmark their own approaches. The code, trained models, and the data will be shared.

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Nikolay Burlutskiy, Marija Kekic, Jordi de la Torre, Philipp Plewa, Mehdi Boroumand, Julia Jurkowska, Borjan Venovski, Maria Chiara Biagi, Yeman Brhane Hagos, Roksana Malinowska-Traczyk, Yibo Wang, Jacek Zalewski, Paula Sawczuk, Karlo Pintarić, Fariba Yousefi, Leif Hultin. 2024-11-26. MiceBoneChallenge: Micro-CT public dataset and six solutions for automatic growth plate detection in micro-CT mice bone scans. https://arxiv.org/abs/2411.17260

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