The segmentation of pelvic fracture fragments in CT and X-ray images is crucial for trauma diagnosis, surgical planning, and intraoperative guidance. However, accurately and efficiently delineating the bone fragments remains a significant challenge due to complex anatomy and imaging limitations. The PENGWIN challenge, organized as a MICCAI 2024 satellite event, aimed to advance automated fracture segmentation by benchmarking state-of-the-art algorithms on these complex tasks. A diverse dataset of 150 CT scans was collected from multiple clinical centers, and a large set of simulated X-ray images was generated using the DeepDRR method. Final submissions from 16 teams worldwide were evaluated under a rigorous multi-metric testing scheme. The top-performing CT algorithm achieved an average fragment-wise intersection over union (IoU) of 0.930, demonstrating satisfactory accuracy. However, in the X-ray task, the best algorithm achieved an IoU of 0.774, which is promising but not yet sufficient for intra-operative decision-making, reflecting the inherent challenges of fragment overlap in projection imaging. Beyond the quantitative evaluation, the challenge revealed methodological diversity in algorithm design. Variations in instance representation, such as primary-secondary classification versus boundary-core separation, led to differing segmentation strategies. Despite promising results, the challenge also exposed inherent uncertainties in fragment definition, particularly in cases of incomplete fractures. These findings suggest that interactive segmentation approaches, integrating human decision-making with task-relevant information, may be essential for improving model reliability and clinical applicability.

Tooth segmentation in Cone-Beam Computed Tomography (CBCT) remains challenging, especially for fine structures like root apices, which is critical for assessing root resorption in orthodontics. We introduce GEPAR3D, a novel approach that unifies instance detection and multi-class segmentation into a single step tailored to improve root segmentation. Our method integrates a Statistical Shape Model of dentition as a geometric prior, capturing anatomical context and morphological consistency without enforcing restrictive adjacency constraints. We leverage a deep watershed method, modeling each tooth as a continuous 3D energy basin encoding voxel distances to boundaries. This instance-aware representation ensures accurate segmentation of narrow, complex root apices. Trained on publicly available CBCT scans from a single center, our method is evaluated on external test sets from two in-house and two public medical centers. GEPAR3D achieves the highest overall segmentation performance, averaging a Dice Similarity Coefficient (DSC) of 95.0% (+2.8% over the second-best method) and increasing recall to 95.2% (+9.5%) across all test sets. Qualitative analyses demonstrated substantial improvements in root segmentation quality, indicating significant potential for more accurate root resorption assessment and enhanced clinical decision-making in orthodontics. We provide the implementation and dataset at github.com/tomek1911/GEPAR3D .

In recent years, artificial intelligence has significantly advanced medical image segmentation. Nonetheless, challenges remain, including efficient 3D medical image processing across diverse modalities and handling data variability. In this work, we introduce Hierarchical Soft Mixture-of-Experts (HoME), a two-level token-routing layer for efficient long-context modeling, specifically designed for 3D medical image segmentation. Built on the Mamba Selective State Space Model (SSM) backbone, HoME enhances sequential modeling through adaptive expert routing. In the first level, a Soft Mixture-of-Experts (SMoE) layer partitions input sequences into local groups, routing tokens to specialized per-group experts for localized feature extraction. The second level aggregates these outputs through a global SMoE layer, enabling cross-group information fusion and global context refinement. This hierarchical design, combining local expert routing with global expert refinement, enhances generalizability and segmentation performance, surpassing state-of-the-art results across datasets from the three most widely used 3D medical imaging modalities and varying data qualities. The code is publicly available at https://github.com/gmum/MambaHoME.

Analysis of 3D segmentation models, especially in the context of medical imaging, is often limited to segmentation performance metrics that overlook the crucial aspect of explainability and bias. Currently, effectively explaining these models with saliency maps is challenging due to the high dimensions of input images multiplied by the ever-growing number of segmented class labels. To this end, we introduce AGG2Exp, a methodology for aggregating fine-grained voxel attributions of the segmentation model's pre-dictions. Unlike classical explanation methods that primar-ily focus on the local feature attribution, Agg2 Exr enables a more comprehensive global view on the importance of predicted segments in 3D images. Our benchmarking exper-iments show that gradient-based voxel attributions are more faithful to the model's predictions than perturbation-based explanations. As a concrete use-case, we apply AGG2Exp to discover knowledge acquired by the Swin UNEt TRans-former model trained on the TotalSegmentator v2 dataset for segmenting anatomical structures in computed tomogra-phy medical images. AGG2Exp facilitates the explanatory analysis of large segmentation models beyond their predictive performance. The source code is publicly available at https://github.com/mi2datalab/agg2exp.

Computer-assisted surgical (CAS) systems enhance surgical execution and outcomes by providing advanced support to surgeons. These systems often rely on deep learning models trained on complex, challenging-to-annotate data. While synthetic data generation can address these challenges, enhancing the realism of such data is crucial. This work introduces a multi-stage pipeline for generating realistic synthetic data, featuring a fully-fledged surgical simulator that automatically produces all necessary annotations for modern CAS systems. This simulator generates a wide set of annotations that surpass those available in pub-lic synthetic datasets. Additionally, it offers a more complex and realistic simulation of surgical interactions, including the dynamics between surgical instruments and de-formable anatomical environments, outperforming existing approaches. To further bridge the visual gap between synthetic and real data, we propose a lightweight and flexible image-to-image translation method based on Stable Diffusion (SD) and Low-Rank Adaptation (LoRA). This method leverages a limited amount of annotated data, enables efficient training, and maintains the integrity of annotations generated by our simulator. The proposed pipeline is exper-imentally validated and can translate synthetic images into images with real-world characteristics, which can generalize to real-world context, thereby improving both training and CAS guidance. The code and the dataset are available at https://github.com/SanoScience/SimuScope.

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery, including: which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery or during live surgery. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a particularly challenging task when compared to other minimally invasive surgeries due to: the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. The top performing model for step recognition utilised a transformer based architecture, uniquely using an autoregressive decoder with a positional encoding input. The top performing model for instrument recognition utilised a spatial encoder followed by a temporal encoder, which uniquely used a 2-layer temporal architecture. In both cases, these models outperformed purely spatial based models, illustrating the importance of sequential and temporal information. This PitVis-2023 therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

Twin-to-Twin Transfusion Syndrome (TTTS) is a rare condition that affects about 15% of monochorionic pregnancies, in which identical twins share a single placenta. Fetoscopic laser photocoagulation (FLP) is the standard treatment for TTTS, which significantly improves the survival of fetuses. The aim of FLP is to identify abnormal connections between blood vessels and to laser ablate them in order to equalize blood supply to both fetuses. However, performing fetoscopic surgery is challenging due to limited visibility, a narrow field of view, and significant variability among patients and domains. In order to enhance the visualization of placental vessels during surgery, we propose TTTSNet, a network architecture designed for real-time and accurate placental vessel segmentation. Our network architecture incorporates a novel channel attention module and multi-scale feature fusion module to precisely segment tiny placental vessels. To address the challenges posed by FLP-specific fiberscope and amniotic sac-based artifacts, we employed novel data augmentation techniques. These techniques simulate various artifacts, including laser pointer, amniotic sac particles, and structural and optical fiber artifacts. By incorporating these simulated artifacts during training, our network architecture demonstrated robust generalizability. We trained TTTSNet on a publicly available dataset of 2060 video frames from 18 independent fetoscopic procedures and evaluated it on a multi-center external dataset of 24 in-vivo procedures with a total of 2348 video frames. Our method achieved significant performance improvements compared to state-of-the-art methods, with a mean Intersection over Union of 78.26% for all placental vessels and 73.35% for a subset of tiny placental vessels. Moreover, our method achieved 172 and 152 frames per second on an A100 GPU, and Clara AGX, respectively. This potentially opens the door to real-time application during surgical procedures. The code is publicly available at https://github.com/SanoScience/TTTSNet.

Segmentation is a critical step in analyzing the developing human fetal brain. There have been vast improvements in automatic segmentation methods in the past several years, and the Fetal Brain Tissue Annotation (FeTA) Challenge 2021 helped to establish an excellent standard of fetal brain segmentation. However, FeTA 2021 was a single center study, limiting real-world clinical applicability and acceptance. The multi-center FeTA Challenge 2022 focused on advancing the generalizability of fetal brain segmentation algorithms for magnetic resonance imaging (MRI). In FeTA 2022, the training dataset contained images and corresponding manually annotated multi-class labels from two imaging centers, and the testing data contained images from these two centers as well as two additional unseen centers. The multi-center data included different MR scanners, imaging parameters, and fetal brain super-resolution algorithms applied. 16 teams participated and 17 algorithms were evaluated. Here, the challenge results are presented, focusing on the generalizability of the submissions. Both in- and out-of-domain, the white matter and ventricles were segmented with the highest accuracy (Top Dice scores: 0.89, 0.87 respectively), while the most challenging structure remains the grey matter (Top Dice score: 0.75) due to anatomical complexity. The top 5 average Dices scores ranged from 0.81-0.82, the top 5 average percentile Hausdorff distance values ranged from 2.3-2.5mm, and the top 5 volumetric similarity scores ranged from 0.90-0.92. The FeTA Challenge 2022 was able to successfully evaluate and advance generalizability of multi-class fetal brain tissue segmentation algorithms for MRI and it continues to benchmark new algorithms.

Training deep neural networks for 3D segmentation tasks can be challenging, often requiring efficient and effective strategies to improve model performance. In this study, we introduce a novel approach, DeCode, that utilizes label-derived features for model conditioning to support the decoder in the reconstruction process dynamically, aiming to enhance the efficiency of the training process. DeCode focuses on improving 3D segmentation performance through the incorporation of conditioning embedding with learned numerical representation of 3D-label shape features. Specifically, we develop an approach, where conditioning is applied during the training phase to guide the network toward robust segmentation. When labels are not available during inference, our model infers the necessary conditioning embedding directly from the input data, thanks to a feed-forward network learned during the training phase. This approach is tested using synthetic data and cone-beam computed tomography (CBCT) images of teeth. For CBCT, three datasets are used: one publicly available and two in-house. Our results show that DeCode significantly outperforms traditional, unconditioned models in terms of generalization to unseen data, achieving higher accuracy at a reduced computational cost. This work represents the first of its kind to explore conditioning strategies in 3D data segmentation, offering a novel and more efficient method for leveraging annotated data. Our code, pre-trained models are publicly available at https://github.com/SanoScience/DeCode .

Fetoscopy laser photocoagulation is a widely adopted procedure for treating Twin-to-Twin Transfusion Syndrome (TTTS). The procedure involves photocoagulation pathological anastomoses to restore a physiological blood exchange among twins. The procedure is particularly challenging, from the surgeon's side, due to the limited field of view, poor manoeuvrability of the fetoscope, poor visibility due to amniotic fluid turbidity, and variability in illumination. These challenges may lead to increased surgery time and incomplete ablation of pathological anastomoses, resulting in persistent TTTS. Computer-assisted intervention (CAI) can provide TTTS surgeons with decision support and context awareness by identifying key structures in the scene and expanding the fetoscopic field of view through video mosaicking. Research in this domain has been hampered by the lack of high-quality data to design, develop and test CAI algorithms. Through the Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge, which was organized as part of the MICCAI2021 Endoscopic Vision (EndoVis) challenge, we released the first large-scale multi-center TTTS dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms with a focus on creating drift-free mosaics from long duration fetoscopy videos. For this challenge, we released a dataset of 2060 images, pixel-annotated for vessels, tool, fetus and background classes, from 18 in-vivo TTTS fetoscopy procedures and 18 short video clips of an average length of 411 frames for developing placental scene segmentation and frame registration for mosaicking techniques. Seven teams participated in this challenge and their model performance was assessed on an unseen test dataset of 658 pixel-annotated images from 6 fetoscopic procedures and 6 short clips. For the segmentation task, overall baseline performed was the top performing (aggregated mIoU of 0.6763) and was the best on the vessel class (mIoU of 0.5817) while team RREB was the best on the tool (mIoU of 0.6335) and fetus (mIoU of 0.5178) classes. For the registration task, overall the baseline performed better than team SANO with an overall mean 5-frame SSIM of 0.9348. Qualitatively, it was observed that team SANO performed better in planar scenarios, while baseline was better in non-planner scenarios. The detailed analysis showed that no single team outperformed on all 6 test fetoscopic videos. The challenge provided an opportunity to create generalized solutions for fetoscopic scene understanding and mosaicking. In this paper, we present the findings of the FetReg2021 challenge, alongside reporting a detailed literature review for CAI in TTTS fetoscopy. Through this challenge, its analysis and the release of multi-center fetoscopic data, we provide a benchmark for future research in this field.

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 multicenter 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 post-processing (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.

Spina Bifida (SB) is a birth defect developed during the early stage of pregnancy in which there is incomplete closing of the spine around the spinal cord. The growing interest in fetoscopic Spina-Bifida repair, which is performed in fetuses who are still in the pregnant uterus, prompts the need for appropriate training. The learning curve for such procedures is steep and requires excellent procedural skills. Computer-based virtual reality (VR) simulation systems offer a safe, cost-effective, and configurable training environment free from ethical and patient safety issues. However, to the best of our knowledge, there are currently no commercial or experimental VR training simulation systems available for fetoscopic SB-repair procedures. In this paper, we propose a novel VR simulator for core manual skills training for SB-repair. An initial simulation realism validation study was carried out by obtaining subjective feedback (face and content validity) from 14 clinicians. The overall simulation realism was on average marked 4.07 on a 5-point Likert scale (1 - ‘very unrealistic’, 5 - ‘very realistic’). Its usefulness as a training tool for SB-repair as well as in learning fundamental laparoscopic skills was marked 4.63 and 4.80, respectively. These results indicate that VR simulation of fetoscopic procedures may contribute to surgical training without putting fetuses and their mothers at risk. It could also facilitate wider adaptation of fetoscopic procedures in place of much more invasive open fetal surgeries.

Predicting fetal weight at birth is an important aspect of perinatal care, particularly in the context of antenatal management, which includes the planned timing and the mode of delivery. Accurate prediction of weight using prenatal ultrasound is challenging as it requires images of specific fetal body parts during advanced pregnancy which is difficult to capture due to poor quality of images caused by the lack of amniotic fluid. As a consequence, predictions which rely on standard methods often suffer from significant errors. In this paper we propose the Residual Transformer Module which extends a 3D ResNet-based network for analysis of 2D+t spatio-temporal ultrasound video scans. Our end-to-end method, called BabyNet, automatically predicts fetal birth weight based on fetal ultrasound video scans. We evaluate BabyNet using a dedicated clinical set comprising 225 2D fetal ultrasound videos of pregnancies from 75 patients performed one day prior to delivery. Experimental results show that BabyNet outperforms several state-of-the-art methods and estimates the weight at birth with accuracy comparable to human experts. Furthermore, combining estimates provided by human experts with those computed by BabyNet yields the best results, outperforming either of other methods by a significant margin. The source code of BabyNet is available at https://github.com/SanoScience/BabyNet.