Parkinson's disease ranks as the second most prevalent neurodegenerative disorder globally. This research aims to develop a system leveraging Mixed Reality capabilities for tracking and assessing eye movements. In this paper, we present a medical scenario and outline the development of an application designed to capture eye-tracking signals through Mixed Reality technology for the evaluation of neurodegenerative diseases. Additionally, we introduce a pipeline for extracting clinically relevant features from eye-gaze analysis, describing the capabilities of the proposed system from a medical perspective. The study involved a cohort of healthy control individuals and patients suffering from Parkinson's disease, showcasing the feasibility and potential of the proposed technology for non-intrusive monitoring of eye movement patterns for the diagnosis of neurodegenerative diseases. Clinical relevance - Developing a non-invasive biomarker for Parkinson's disease is urgently needed to accurately detect the disease's onset. This would allow for the timely introduction of neuroprotective treatment at the earliest stage and enable the continuous monitoring of intervention outcomes. The ability to detect subtle changes in eye movements allows for early diagnosis, offering a critical window for intervention before more pronounced symptoms emerge. Eye tracking provides objective and quantifiable biomarkers, ensuring reliable assessments of disease progression and cognitive function. The eye gaze analysis using Mixed Reality glasses is wireless, facilitating convenient assessments in both home and hospital settings. The approach offers the advantage of utilizing hardware that requires no additional specialized attachments, enabling examinations through personal eyewear.
Cancer is one of the leading causes of death globally, and early diagnosis is crucial for patient survival. Deep learning algorithms have great potential for automatic cancer analysis. Artificial intelligence has achieved high performance in recognizing and segmenting single lesions. However, diagnosing multiple lesions remains a challenge. This study examines and compares various neural network architectures and training strategies for automatically segmentation of cancer lesions using PET/CT images from the head, neck, and whole body. The authors analyzed datasets from the AutoPET and HECKTOR challenges, exploring popular single-step segmentation architectures and presenting a two-step approach. The results indicate that the V-Net and nnU-Net models were the most effective for their respective datasets. The results for the HECKTOR dataset ranged from 0.75 to 0.76 for the aggregated Dice coefficient. Eliminating cancer-free cases from the AutoPET dataset was found to improve the performance of most models. In the case of AutoPET data, the average segmentation efficiency after training only on images containing cancer lesions increased from 0.55 to 0.66 for the classic Dice coefficient and from 0.65 to 0.73 for the aggregated Dice coefficient. The research demonstrates the potential of artificial intelligence in precise oncological diagnostics and may contribute to the development of more targeted and effective cancer assessment techniques.
The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset and invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. TopCoW dataset was the first public dataset with voxel-level annotations for CoW's 13 vessel components, made possible by virtual-reality (VR) technology. It was also the first dataset with paired MRA and CTA from the same patients. TopCoW challenge aimed to tackle the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant's topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically.
Automatic aorta segmentation from 3-D medical volumes is an important yet difficult task. Several factors make the problem challenging, e.g. the possibility of aortic dissection or the difficulty with segmenting and annotating the small branches. This work presents a contribution by the MedGIFT team to the SEG.A challenge organized during the MICCAI 2023 conference. We propose a fully automated algorithm based on deep encoder-decoder architecture. The main assumption behind our work is that data preprocessing and augmentation are much more important than the deep architecture, especially in low data regimes. Therefore, the solution is based on a variant of traditional convolutional U-Net. The proposed solution achieved a Dice score above 0.9 for all testing cases with the highest stability among all participants. The method scored 1st, 4th, and 3rd in terms of the clinical evaluation, quantitative results, and volumetric meshing quality, respectively. We freely release the source code, pretrained model, and provide access to the algorithm on the Grand-Challenge platform.
The design of personalized cranial implants is a challenging and tremendous task that has become a hot topic in terms of process automation with the use of deep learning techniques. The main challenge is associated with the high diversity of possible cranial defects. The lack of appropriate data sources negatively influences the data-driven nature of deep learning algorithms. Hence, one of the possible solutions to overcome this problem is to rely on synthetic data. In this work, we propose three volumetric variations of deep generative models to augment the dataset by generating synthetic skulls, i.e. Wasserstein Generative Adversarial Network with Gradient Penalty (WGAN-GP), WGAN-GP hybrid with Variational Autoencoder pretraining (VAE/WGAN-GP) and Introspective Variational Autoencoder (IntroVAE). We show that it is possible to generate dozens of thousands of defective skulls with compatible defects that achieve a trade-off between defect heterogeneity and the realistic shape of the skull. We evaluate obtained synthetic data quantitatively by defect segmentation with the use of V-Net and qualitatively by their latent space exploration. We show that the synthetically generated skulls highly improve the segmentation process compared to using only the original unaugmented data. The generated skulls may improve the automatic design of personalized cranial implants for real medical cases.
Each year thousands of people suffer from various types of cranial injuries and require personalized implants whose manual design is expensive and time-consuming. Therefore, an automatic, dedicated system to increase the availability of personalized cranial reconstruction is highly desirable. The problem of the automatic cranial defect reconstruction can be formulated as the shape completion task and solved using dedicated deep networks. Currently, the most common approach is to use the volumetric representation and apply deep networks dedicated to image segmentation. However, this approach has several limitations and does not scale well into high-resolution volumes, nor takes into account the data sparsity. In our work, we reformulate the problem into a point cloud completion task. We propose an iterative, transformer-based method to reconstruct the cranial defect at any resolution while also being fast and resource-efficient during training and inference. We compare the proposed methods to the state-of-the-art volumetric approaches and show superior performance in terms of GPU memory consumption while maintaining high-quality of the reconstructed defects.
The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for research and clinical applications. Advances in computing, deep learning, and availability of large WSI datasets have revolutionised WSI analysis. Therefore, the current state-of-the-art in WSI registration is unclear. To address this, we conducted the ACROBAT challenge, based on the largest WSI registration dataset to date, including 4,212 WSIs from 1,152 breast cancer patients. The challenge objective was to align WSIs of tissue that was stained with routine diagnostic immunohistochemistry to its H&E-stained counterpart. We compare the performance of eight WSI registration algorithms, including an investigation of the impact of different WSI properties and clinical covariates. We find that conceptually distinct WSI registration methods can lead to highly accurate registration performances and identify covariates that impact performances across methods. These results establish the current state-of-the-art in WSI registration and guide researchers in selecting and developing methods.
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.
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.
Registration of brain scans with pathologies is difficult, yet important research area. The importance of this task motivated researchers to organize the BraTS-Reg challenge, jointly with IEEE ISBI 2022 and MICCAI 2022 conferences. The organizers introduced the task of aligning pre-operative to follow-up magnetic resonance images of glioma. The main difficulties are connected with the missing data leading to large, nonrigid, and noninvertible deformations. In this work, we describe our contributions to both the editions of the BraTS-Reg challenge. The proposed method is based on combined deep learning and instance optimization approaches. First, the instance optimization enriches the state-of-the-art LapIRN method to improve the generalizability and fine-details preservation. Second, an additional objective function weighting is introduced, based on the inverse consistency. The proposed method is fully unsupervised and exhibits high registration quality and robustness. The quantitative results on the external validation set are: (i) IEEE ISBI 2022 edition: 1.85, and 0.86, (ii) MICCAI 2022 edition: 1.71, and 0.86, in terms of the mean of median absolute error and robustness respectively. The method scored the 1st place during the IEEE ISBI 2022 version of the challenge and the 3rd place during the MICCAI 2022. Future work could transfer the inverse consistency-based weighting directly into the deep network training.