Unified and Semantically Grounded Domain Adaptation for Medical Image Segmentation

Most prior unsupervised domain adaptation approaches for medical image segmentation are narrowly tailored to either the source-accessible setting, where adaptation is guided by source-target alignment, or the source-free setting, which typically resorts to implicit supervision mechanisms such as pseudo-labeling and model distillation. This substantial divergence in methodological designs between the two settings reveals an inherent flaw: the lack of an explicit, structured construction of anatomical knowledge that naturally generalizes across domains and settings. To bridge this longstanding divide, we introduce a unified, semantically grounded framework that supports both source-accessible and source-free adaptation. Fundamentally distinct from all prior works, our framework's adaptability emerges naturally as a direct consequence of the model architecture, without the need for any handcrafted adaptation strategies. Specifically, our model learns a domain-agnostic probabilistic manifold as a global space of anatomical regularities, mirroring how humans establish visual understanding. Thus, the structural content in each image can be interpreted as a canonical anatomy retrieved from the manifold and a spatial transformation capturing individual-specific geometry. This disentangled, interpretable formulation enables semantically meaningful prediction with intrinsic adaptability. Extensive experiments on challenging cardiac and abdominal datasets show that our framework achieves state-of-the-art results in both settings, with source-free performance closely approaching its source-accessible counterpart, a level of consistency rarely observed in prior works. Beyond quantitative improvement, we demonstrate strong interpretability of the proposed framework via manifold traversal for smooth shape manipulation.

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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.

Deep Open Snake Tracker for Vessel Tracing

Vessel tracing by modeling vascular structures in 3D medical images with centerlines and radii can provide useful information for vascular health. Existing algorithms have been developed but there are certain persistent problems such as incomplete or inaccurate vessel tracing, especially in complicated vascular beds like the intracranial arteries. We propose here a deep learning based open curve active contour model (DOST) to trace vessels in 3D images. Initial curves were proposed from a centerline segmentation neural network. Then data-driven machine knowledge was used to predict the stretching direction and vessel radius of the initial curve, while the active contour model (as human knowledge) maintained smoothness and intensity fitness of curves. Finally, considering the nonloop topology of most vasculatures, individually traced vessels were connected into a tree topology by applying a minimum spanning tree algorithm on a global connection graph. We evaluated DOST on a Time-of-Flight (TOF) MRA intracranial artery dataset and demonstrated its superior performance over existing segmentation-based and tracking-based vessel tracing methods. In addition, DOST showed strong adaptability on different imaging modalities (CTA, MR T1 SPACE) and vascular beds (coronary arteries).

Y-net: 3D intracranial artery segmentation using a convolutional autoencoder

Automated segmentation of intracranial arteries on magnetic resonance angiography (MRA) allows for quantification of cerebrovascular features, which provides tools for understanding aging and pathophysiological adaptations of the cerebrovascular system. Using a convolutional autoencoder (CAE) for segmentation is promising as it takes advantage of the autoencoder structure in effective noise reduction and feature extraction by representing high dimensional information with low dimensional latent variables. In this report, an optimized CAE model (Y-net) was trained to learn a 3D segmentation model of intracranial arteries from 49 cases of MRA data. The trained model was shown to perform better than the three traditional segmentation methods in both binary classification and visual evaluation.