arXiv subjects

Ivan Ezhov

Publications and source records attributed to Ivan Ezhov.

At least 19 recordsLinked to original sources

arXiv2026

A unified perspective on wavelength selection for molecular composition inference from diffuse spectroscopy

Optical monitoring of living tissue targeting quantification of molecular composition is an active area of research. In the case of broadband spectroscopy, one can attempt to extract molecular, or more precisely, chromophore concentration from a broad-range spectrum of the reflected light. However, selecting the shortest wavelength range sufficient for quantitative optical monitoring remains an open problem. Various wavelength optimization methods are scattered throughout the literature, however, there is no unified view to date. Our work's motivation is to construct a wavelength selection framework by unifying existing selection approaches and propose a novel projection-based method that allows for the pre-identification of a wavelength range that is adequate for the final selection. The framework specifically focuses on proposing different methods that quantify match or mismatch between the chosen light-matter interaction model, defined by the chosen endmembers (e.g. molecular chromophores), and the measured intensity from the spectroscopic data. To evaluate the framework, we perform a retrospective analysis on a broadband spectroscopy dataset of piglets during an induced hypoxia-ischemia state. Overall, we show that our novel projection-based method can be used for band selection, and that existing approaches can be used in conjunction to select an optimal minimal wavelength set that satisfies biophysical model constraints.

physics.optics↗

arXiv2026

A Physics-Guided Neural Framework for Rheology Measurement from Dynamical Laser Speckles

Critical breakthroughs in the area of biomedicine and materials science increasingly depend on rapid, non-contact methods for viscoelastic characterization. Laser Speckle Rheology (LSR) is positioned to meet this demand, effectively circumventing the speed and invasiveness bottlenecks inherent to traditional mechanical rheometer. However, its application in turbid fluids is severely constrained by multiple scattering, where standard physical inversions rely heavily on precise, sample-specific optical transport parameters that are difficult to measure in situ. To overcome this barrier, we propose a physics-guided deep learning framework that infers a Maxwell relaxation spectrum from the intensity autocorrelation g2(t) and speckle-intensity histogram statistics. The resulting spectrum is then propagated through a Maxwell forward model to predict G'and G'' under physics-consistency constraints. Quantitatively, the framework achieves RMSElog as low as 0.009 against reference and generalizes to previously unseen scattering conditions, preserving physically plausible frequency dependence and G'- G'' phase behavior. It reduces reliance on optical transport parameters that are hard to determine in situ and returns an interpretable generalized Maxwell relaxation spectrum, improving the practicality of LSR in turbid media.

physics.optics↗

arXiv2025

The MICCAI Federated Tumor Segmentation (FeTS) Challenge 2024: Efficient and Robust Aggregation Methods for Federated Learning

We present the design and results of the MICCAI Federated Tumor Segmentation (FeTS) Challenge 2024, which focuses on federated learning (FL) for glioma sub-region segmentation in multi-parametric MRI and evaluates new weight aggregation methods aimed at improving robustness and efficiency. Six participating teams were evaluated using a standardized FL setup and a multi-institutional dataset derived from the BraTS glioma benchmark, consisting of 1,251 training cases, 219 validation cases, and 570 hidden test cases with segmentations for enhancing tumor (ET), tumor core (TC), and whole tumor (WT). Teams were ranked using a cumulative scoring system that considered both segmentation performance, measured by Dice Similarity Coefficient (DSC) and the 95th percentile Hausdorff Distance (HD95), and communication efficiency assessed through the convergence score. A PID-controller-based method achieved the top overall ranking, obtaining mean DSC values of 0.733, 0.761, and 0.751 for ET, TC, and WT, respectively, with corresponding HD95 values of 33.922 mm, 33.623 mm, and 32.309 mm, while also demonstrating the highest communication efficiency with a convergence score of 0.764. These findings advance the state of federated learning for medical imaging, surpassing top-performing methods from previous challenge iterations and highlighting PID controllers as effective mechanisms for stabilizing and optimizing weight aggregation in FL. The challenge code is available at https://github.com/FeTS-AI/Challenge.

cs.CV↗

arXiv2025

Individualizing Glioma Radiotherapy Planning by Optimization of Data and Physics-Informed Discrete Loss

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss, where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation model, which is adapted for complex cases.

physics.med-ph↗

arXiv2025

Efficient Deep Learning-based Forward Solvers for Brain Tumor Growth Models

Glioblastoma, a highly aggressive brain tumor, poses major challenges due to its poor prognosis and high morbidity rates. Partial differential equation-based models offer promising potential to enhance therapeutic outcomes by simulating patient-specific tumor behavior for improved radiotherapy planning. However, model calibration remains a bottleneck due to the high computational demands of optimization methods like Monte Carlo sampling and evolutionary algorithms. To address this, we recently introduced an approach leveraging a neural forward solver with gradient-based optimization to significantly reduce calibration time. This approach requires a highly accurate and fully differentiable forward model. We investigate multiple architectures, including (i) an enhanced TumorSurrogate, (ii) a modified nnU-Net, and (iii) a 3D Vision Transformer (ViT). The nnU-Net achieved the best overall results, excelling in both tumor outline matching and voxel-level prediction of tumor cell concentration. It yielded the lowest MSE in tumor cell concentration compared to ground truth numerical simulation and the highest Dice score across all tumor cell concentration thresholds. Our study demonstrates significant enhancement in forward solver performance and outlines important future research directions.

cs.CV↗

arXiv2025

Addressing Annotation Scarcity in Hyperspectral Brain Image Segmentation with Unsupervised Domain Adaptation

This work presents a novel deep learning framework for segmenting cerebral vasculature in hyperspectral brain images. We address the critical challenge of severe label scarcity, which impedes conventional supervised training. Our approach utilizes a novel unsupervised domain adaptation methodology, using a small, expert-annotated ground truth alongside unlabeled data. Quantitative and qualitative evaluations confirm that our method significantly outperforms existing state-of-the-art approaches, demonstrating the efficacy of domain adaptation for label-scarce biomedical imaging tasks.

cs.CV↗

arXiv2025

A Lightweight Optimization Framework for Estimating 3D Brain Tumor Infiltration

Glioblastoma, the most aggressive primary brain tumor, poses a severe clinical challenge due to its diffuse microscopic infiltration, which remains largely undetected on standard MRI. As a result, current radiotherapy planning employs a uniform 15 mm margin around the resection cavity, failing to capture patient-specific tumor spread. Tumor growth modeling offers a promising approach to reveal this hidden infiltration. However, methods based on partial differential equations or physics-informed neural networks tend to be computationally intensive or overly constrained, limiting their clinical adaptability to individual patients. In this work, we propose a lightweight, rapid, and robust optimization framework that estimates the 3D tumor concentration by fitting it to MRI tumor segmentations while enforcing a smooth concentration landscape. This approach achieves superior tumor recurrence prediction on 192 brain tumor patients across two public datasets, outperforming state-of-the-art baselines while reducing runtime from 30 minutes to less than one minute. Furthermore, we demonstrate the framework's versatility and adaptability by showing its ability to seamlessly integrate additional imaging modalities or physical constraints.

physics.med-ph↗

arXiv2025

From Fiber Tracts to Tumor Spread: Biophysical Modeling of Butterfly Glioma Growth Using Diffusion Tensor Imaging

Butterfly tumors are a distinct class of gliomas that span the corpus callosum, producing a characteristic butterfly-shaped appearance on MRI. The distinctive growth pattern of these tumors highlights how white matter fibers and structural connectivity influence brain tumor cell migration. To investigate this relation, we applied biophysical tumor growth models to a large patient cohort, systematically comparing models that incorporate fiber tract information with those that do not. Our results demonstrate that including fiber orientation data significantly improves model accuracy, particularly for a subset of butterfly tumors. These findings highlight the critical role of white matter architecture in tumor spread and suggest that integrating fiber tract information can enhance the precision of radiotherapy target volume delineation.

physics.med-ph↗

arXiv2025

BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis

BrainLesion Suite is a versatile toolkit for building modular brain lesion image analysis pipelines in Python. Following Pythonic principles, BrainLesion Suite is designed to provide a 'brainless' development experience, minimizing cognitive effort and streamlining the creation of complex workflows for clinical and scientific practice. At its core is an adaptable preprocessing module that performs co-registration, atlas registration, and optional skull-stripping and defacing on arbitrary multi-modal input images. BrainLesion Suite leverages algorithms from the BraTS challenge to synthesize missing modalities, inpaint lesions, and generate pathology-specific tumor segmentations. BrainLesion Suite also enables quantifying segmentation model performance, with tools such as panoptica to compute lesion-wise metrics. Although BrainLesion Suite was originally developed for image analysis pipelines of brain lesions such as glioma, metastasis, and multiple sclerosis, it can be adapted for other biomedical image analysis applications. The individual BrainLesion Suite packages and tutorials are accessible on GitHub.

cs.CV↗

arXiv2025

Analysis of the MICCAI Brain Tumor Segmentation -- Metastases (BraTS-METS) 2025 Lighthouse Challenge: Brain Metastasis Segmentation on Pre- and Post-treatment MRI

Despite continuous advancements in cancer treatment, brain metastatic disease remains a significant complication of primary cancer and is associated with an unfavorable prognosis. One approach for improving diagnosis, management, and outcomes is to implement algorithms based on artificial intelligence for the automated segmentation of both pre- and post-treatment MRI brain images. Such algorithms rely on volumetric criteria for lesion identification and treatment response assessment, which are still not available in clinical practice. Therefore, it is critical to establish tools for rapid volumetric segmentations methods that can be translated to clinical practice and that are trained on high quality annotated data. The BraTS-METS 2025 Lighthouse Challenge aims to address this critical need by establishing inter-rater and intra-rater variability in dataset annotation by generating high quality annotated datasets from four individual instances of segmentation by neuroradiologists while being recorded on video (two instances doing "from scratch" and two instances after AI pre-segmentation). This high-quality annotated dataset will be used for testing phase in 2025 Lighthouse challenge and will be publicly released at the completion of the challenge. The 2025 Lighthouse challenge will also release the 2023 and 2024 segmented datasets that were annotated using an established pipeline of pre-segmentation, student annotation, two neuroradiologists checking, and one neuroradiologist finalizing the process. It builds upon its previous edition by including post-treatment cases in the dataset. Using these high-quality annotated datasets, the 2025 Lighthouse challenge plans to test benchmark algorithms for automated segmentation of pre-and post-treatment brain metastases (BM), trained on diverse and multi-institutional datasets of MRI images obtained from patients with brain metastases.

q-bio.OT↗

arXiv2025

BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023

Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children. The five-year survival rate for high-grade glioma in children is less than 20%. The development of new treatments is dependent upon multi-institutional collaborative clinical trials requiring reproducible and accurate centralized response assessment. We present the results of the BraTS-PEDs 2023 challenge, the first Brain Tumor Segmentation (BraTS) challenge focused on pediatric brain tumors. This challenge utilized data acquired from multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. BraTS-PEDs 2023 aimed to evaluate volumetric segmentation algorithms for pediatric brain gliomas from magnetic resonance imaging using standardized quantitative performance evaluation metrics employed across the BraTS 2023 challenges. The top-performing AI approaches for pediatric tumor analysis included ensembles of nnU-Net and Swin UNETR, Auto3DSeg, or nnU-Net with a self-supervised framework. The BraTSPEDs 2023 challenge fostered collaboration between clinicians (neuro-oncologists, neuroradiologists) and AI/imaging scientists, promoting faster data sharing and the development of automated volumetric analysis techniques. These advancements could significantly benefit clinical trials and improve the care of children with brain tumors.

eess.IV↗

arXiv2025

Redefining spectral unmixing for in-vivo brain tissue analysis from hyperspectral imaging

In this paper, we propose a methodology for extracting molecular tumor biomarkers from hyperspectral imaging (HSI), an emerging technology for intraoperative tissue assessment. To achieve this, we employ spectral unmixing, allowing to decompose the spectral signals recorded by the HSI camera into their constituent molecular components. Traditional unmixing approaches are based on physical models that establish a relationship between tissue molecules and the recorded spectra. However, these methods commonly assume a linear relationship between the spectra and molecular content, which does not capture the whole complexity of light-matter interaction. To address this limitation, we introduce a novel unmixing procedure that allows to take into account non-linear optical effects while preserving the computational benefits of linear spectral unmixing. We validate our methodology on an in-vivo brain tissue HSI dataset and demonstrate that the extracted molecular information leads to superior classification performance.

physics.med-ph↗

arXiv2025

BraTS orchestrator : Democratizing and Disseminating state-of-the-art brain tumor image analysis

The Brain Tumor Segmentation (BraTS) cluster of challenges has significantly advanced brain tumor image analysis by providing large, curated datasets and addressing clinically relevant tasks. However, despite its success and popularity, algorithms and models developed through BraTS have seen limited adoption in both scientific and clinical communities. To accelerate their dissemination, we introduce BraTS orchestrator, an open-source Python package that provides seamless access to state-of-the-art segmentation and synthesis algorithms for diverse brain tumors from the BraTS challenge ecosystem. Available on GitHub (https://github.com/BrainLesion/BraTS), the package features intuitive tutorials designed for users with minimal programming experience, enabling both researchers and clinicians to easily deploy winning BraTS algorithms for inference. By abstracting the complexities of modern deep learning, BraTS orchestrator democratizes access to the specialized knowledge developed within the BraTS community, making these advances readily available to broader neuro-radiology and neuro-oncology audiences.

eess.IV↗

arXiv2025

Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge

We describe the design and results from the BraTS 2023 Intracranial Meningioma Segmentation Challenge. The BraTS Meningioma Challenge differed from prior BraTS Glioma challenges in that it focused on meningiomas, which are typically benign extra-axial tumors with diverse radiologic and anatomical presentation and a propensity for multiplicity. Nine participating teams each developed deep-learning automated segmentation models using image data from the largest multi-institutional systematically expert annotated multilabel multi-sequence meningioma MRI dataset to date, which included 1000 training set cases, 141 validation set cases, and 283 hidden test set cases. Each case included T2, FLAIR, T1, and T1Gd brain MRI sequences with associated tumor compartment labels delineating enhancing tumor, non-enhancing tumor, and surrounding non-enhancing FLAIR hyperintensity. Participant automated segmentation models were evaluated and ranked based on a scoring system evaluating lesion-wise metrics including dice similarity coefficient (DSC) and 95% Hausdorff Distance. The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0.976, 0.976, and 0.964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0.899, 0.904, and 0.871, respectively. These results serve as state-of-the-art benchmarks for future pre-operative meningioma automated segmentation algorithms. Additionally, we found that 1286 of 1424 cases (90.3%) had at least 1 compartment voxel abutting the edge of the skull-stripped image edge, which requires further investigation into optimal pre-processing face anonymization steps.

eess.IV↗

arXiv2024

MultiOrg: A Multi-rater Organoid-detection Dataset

High-throughput image analysis in the biomedical domain has gained significant attention in recent years, driving advancements in drug discovery, disease prediction, and personalized medicine. Organoids, specifically, are an active area of research, providing excellent models for human organs and their functions. Automating the quantification of organoids in microscopy images would provide an effective solution to overcome substantial manual quantification bottlenecks, particularly in high-throughput image analysis. However, there is a notable lack of open biomedical datasets, in contrast to other domains, such as autonomous driving, and, notably, only few of them have attempted to quantify annotation uncertainty. In this work, we present MultiOrg a comprehensive organoid dataset tailored for object detection tasks with uncertainty quantification. This dataset comprises over 400 high-resolution 2d microscopy images and curated annotations of more than 60,000 organoids. Most importantly, it includes three label sets for the test data, independently annotated by two experts at distinct time points. We additionally provide a benchmark for organoid detection, and make the best model available through an easily installable, interactive plugin for the popular image visualization tool Napari, to perform organoid quantification.

cs.CV↗

arXiv2024

The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space.The BraTS-METS 2023 challenge successfully curated well-annotated, diverse datasets and identified common errors, facilitating the translation of BM segmentation across varied clinical environments and providing personalized volumetric reports to patients undergoing BM treatment.

q-bio.OT↗

arXiv2024

Neural Network Surrogate and Projected Gradient Descent for Fast and Reliable Finite Element Model Calibration: a Case Study on an Intervertebral Disc

Accurate calibration of finite element (FE) models is essential across various biomechanical applications, including human intervertebral discs (IVDs), to ensure their reliability and use in diagnosing and planning treatments. However, traditional calibration methods are computationally intensive, requiring iterative, derivative-free optimization algorithms that often take days to converge. This study addresses these challenges by introducing a novel, efficient, and effective calibration method demonstrated on a human L4-L5 IVD FE model as a case study using a neural network (NN) surrogate. The NN surrogate predicts simulation outcomes with high accuracy, outperforming other machine learning models, and significantly reduces the computational cost associated with traditional FE simulations. Next, a Projected Gradient Descent (PGD) approach guided by gradients of the NN surrogate is proposed to efficiently calibrate FE models. Our method explicitly enforces feasibility with a projection step, thus maintaining material bounds throughout the optimization process. The proposed method is evaluated against SOTA Genetic Algorithm and inverse model baselines on synthetic and in vitro experimental datasets. Our approach demonstrates superior performance on synthetic data, achieving an MAE of 0.06 compared to the baselines' MAE of 0.18 and 0.54, respectively. On experimental specimens, our method outperforms the baseline in 5 out of 6 cases. While our approach requires initial dataset generation and surrogate training, these steps are performed only once, and the actual calibration takes under three seconds. In contrast, traditional calibration time scales linearly with the number of specimens, taking up to 8 days in the worst-case. Such efficiency paves the way for applying more complex FE models, potentially extending beyond IVDs, and enabling accurate patient-specific simulations.

cs.LG↗

arXiv2024

Cross-domain and Cross-dimension Learning for Image-to-Graph Transformers

Direct image-to-graph transformation is a challenging task that involves solving object detection and relationship prediction in a single model. Due to this task's complexity, large training datasets are rare in many domains, making the training of deep-learning methods challenging. This data sparsity necessitates transfer learning strategies akin to the state-of-the-art in general computer vision. In this work, we introduce a set of methods enabling cross-domain and cross-dimension learning for image-to-graph transformers. We propose (1) a regularized edge sampling loss to effectively learn object relations in multiple domains with different numbers of edges, (2) a domain adaptation framework for image-to-graph transformers aligning image- and graph-level features from different domains, and (3) a projection function that allows using 2D data for training 3D transformers. We demonstrate our method's utility in cross-domain and cross-dimension experiments, where we utilize labeled data from 2D road networks for simultaneous learning in vastly different target domains. Our method consistently outperforms standard transfer learning and self-supervised pretraining on challenging benchmarks, such as retinal or whole-brain vessel graph extraction.

cs.CV↗