Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Weakly-supervised Biomechanically-constrained CT/MRI Registration of the Spine

CT and MRI are two of the most informative modalities in spinal diagnostics and treatment planning. CT is useful when analysing bony structures, while MRI gives information about the soft tissue. Thus, fusing the information of both modalities can be very beneficial. Registration is the first step for this fusion. While the soft tissues around the vertebra are deformable, each vertebral body is constrained to move rigidly. We propose a weakly-supervised deep learning framework that preserves the rigidity and the volume of each vertebra while maximizing the accuracy of the registration. To achieve this goal, we introduce anatomy-aware losses for training the network. We specifically design these losses to depend only on the CT label maps since automatic vertebra segmentation in CT gives more accurate results contrary to MRI. We evaluate our method on an in-house dataset of 167 patients. Our results show that adding the anatomy-aware losses increases the plausibility of the inferred transformation while keeping the accuracy untouched.

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks, in part because of the lack of availability of such diverse data. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration benchmark for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, and the results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias.

Patient-specific virtual spine straightening and vertebra inpainting: An automatic framework for osteoplasty planning

Symptomatic spinal vertebral compression fractures (VCFs) often require osteoplasty treatment. A cement-like material is injected into the bone to stabilize the fracture, restore the vertebral body height and alleviate pain. Leakage is a common complication and may occur due to too much cement being injected. In this work, we propose an automated patient-specific framework that can allow physicians to calculate an upper bound of cement for the injection and estimate the optimal outcome of osteoplasty. The framework uses the patient CT scan and the fractured vertebra label to build a virtual healthy spine using a high-level approach. Firstly, the fractured spine is segmented with a three-step Convolution Neural Network (CNN) architecture. Next, a per-vertebra rigid registration to a healthy spine atlas restores its curvature. Finally, a GAN-based inpainting approach replaces the fractured vertebra with an estimation of its original shape. Based on this outcome, we then estimate the maximum amount of bone cement for injection. We evaluate our framework by comparing the virtual vertebrae volumes of ten patients to their healthy equivalent and report an average error of 3.88$\pm$7.63\%. The presented pipeline offers a first approach to a personalized automatic high-level framework for planning osteoplasty procedures.