Despite academic success, radiomics-based machine learning algorithms have not reached clinical practice, partially due to limited repeatability/reproducibility. To address this issue, this work aims to identify a stable subset of radiomics features in prostate MRI for radiomics modelling. A prospective study was conducted in 43 patients who received a clinical MRI examination and a research exam with repetition of T2-weighted and two different diffusion-weighted imaging (DWI) sequences with repositioning in between. Radiomics feature (RF) extraction was performed from MRI segmentations accounting for intra-rater and inter-rater effects, and three different image normalization methods were compared. Stability of RFs was assessed using the concordance correlation coefficient (CCC) for different comparisons: rater effects, inter-scan (before and after repositioning) and inter-sequence (between the two diffusion-weighted sequences) variability. In total, only 64 out of 321 (~ 20%) extracted features demonstrated stability, defined as CCC ≥ 0.75 in all settings (5 high-b value, 7 ADC- and 52 T2-derived features). For DWI, primarily intensity-based features proved stable with no shape feature passing the CCC threshold. T2-weighted images possessed the largest number of stable features with multiple shape (7), intensity-based (7) and texture features (28). Z-score normalization for high-b value images and muscle-normalization for T2-weighted images were identified as suitable.

Atrial fibrillation, a common cardiac arrhythmia with rapid and irregular atrial electrical activity, requires accurate left atrial segmentation for effective treatment planning. Recently, deep learning methods have gained encouraging success in left atrial segmentation. However, current methodologies critically depend on the assumption of consistently complete centered left atrium as input, which neglects the structural incompleteness and boundary discontinuities arising from random-crop operations during inference. In this paper, we propose BSA-Net, which exploits an adaptive adjustment strategy in both feature position and loss optimization to establish long-range feature relationships and strengthen robust intermediate feature representations in boundary regions. Specifically, we propose a Spatial-adaptive Convolution (SConv) that employs a shuffle operation combined with lightweight convolution to directly establish cross-positional relationships within regions of potential relevance. Moreover, we develop the dual Boundary Prioritized loss, which enhances boundary precision by differentially weighting foreground and background boundaries, thus optimizing complex boundary regions. With the above technologies, the proposed method enjoys a better speed-accuracy trade-off compared to current methods. BSA-Net attains Dice scores of 92.55%, 91.42%, and 84.67% on the LA, Utah, and Waikato datasets, respectively, with a mere 2.16 M parameters-approximately 80% fewer than other contemporary state-of-the-art models. Extensive experimental results on three benchmark datasets have demonstrated that BSA-Net, consistently and significantly outperforms existing state-of-the-art methods.

Cervical spondylosis, a complex and prevalent condition, demands precise and efficient diagnostic techniques for accurate assessment. While MRI offers detailed visualization of cervical spine anatomy, manual interpretation remains labor-intensive and prone to error. To address this, we developed an innovative AI-assisted Expert-based Diagnosis System that automates both segmentation and diagnosis of cervical spondylosis using MRI. Leveraging multi-center datasets of cervical MRI images from patients with cervical spondylosis, our system features a pathology-guided segmentation model capable of accurately segmenting key cervical anatomical structures. The segmentation is followed by an expert-based diagnostic framework that automates the calculation of critical clinical indicators. Our segmentation model achieved an impressive average Dice coefficient exceeding 0.90 across four cervical spinal anatomies and demonstrated enhanced accuracy in herniation areas. Diagnostic evaluation further showcased the system's precision, with the lowest mean average errors (MAE) for the C2-C7 Cobb angle and the Maximum Spinal Cord Compression (MSCC) coefficient. In addition, our method delivered high accuracy, precision, recall, and F1 scores in herniation localization, K-line status assessment, T2 hyperintensity detection, and Kang grading. Comparative analysis and external validation demonstrate that our system outperforms existing methods, establishing a new benchmark for segmentation and diagnostic tasks for cervical spondylosis.

Advances in image registration and machine learning have recently enabled volumetric analysis of \emph{postmortem} brain tissue from conventional photographs of coronal slabs, which are routinely collected in brain banks and neuropathology laboratories worldwide. One caveat of this methodology is the requirement of segmentation of the tissue from photographs, which currently requires costly manual intervention. In this article, we present a deep learning model to automate this process. The automatic segmentation tool relies on a U-Net architecture that was trained with a combination of \textit{(i)}1,414 manually segmented images of both fixed and fresh tissue, from specimens with varying diagnoses, photographed at two different sites; and \textit{(ii)}~2,000 synthetic images with randomized contrast and corresponding masks generated from MRI scans for improved generalizability to unseen photographic setups. Automated model predictions on a subset of photographs not seen in training were analyzed to estimate performance compared to manual labels -- including both inter- and intra-rater variability. Our model achieved a median Dice score over 0.98, mean surface distance under 0.4~mm, and 95\% Hausdorff distance under 1.60~mm, which approaches inter-/intra-rater levels. Our tool is publicly available at surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools.

Background: In the field of radiology and radiotherapy, accurate delineation of tissues and organs plays a crucial role in both diagnostics and therapeutics. While the gold standard remains expert-driven manual segmentation, many automatic segmentation methods are emerging. The evaluation of these methods primarily relies on traditional metrics that only incorporate geometrical properties and fail to adapt to various applications. Aims: This study aims to develop and implement a clinically relevant segmentation metric that can be adapted for use in various medical imaging applications. Methods: Bidirectional local distance was defined, and the points of the test contour were paired with points of the reference contour. After correcting for the distance between the test and reference center of mass, Euclidean distance was calculated between the paired points, and a score was given to each test point. The overall medical similarity index was calculated as the average score across all the test points. For demonstration, we used myoma and prostate datasets; nnUNet neural networks were trained for segmentation. Results: An easy-to-use, sustainable image processing pipeline was created using Python. The code is available in a public GitHub repository along with Google Colaboratory notebooks. The algorithm can handle multislice images with multiple masks per slice. Mask splitting algorithm is also provided that can separate the concave masks. We demonstrate the adaptability with prostate segmentation evaluation. Conclusions: A novel segmentation evaluation metric was implemented, and an open-access image processing pipeline was also provided, which can be easily used for automatic measurement of clinical relevance of medical image segmentation.}

KonfAI is a modular, extensible, and fully configurable deep learning framework specifically designed for medical imaging tasks. It enables users to define complete training, inference, and evaluation workflows through structured YAML configuration files, without modifying the underlying code. This declarative approach enhances reproducibility, transparency, and experimental traceability while reducing development time. Beyond the capabilities of standard pipelines, KonfAI provides native abstractions for advanced strategies including patch-based learning, test-time augmentation, model ensembling, and direct access to intermediate feature representations for deep supervision. It also supports complex multi-model training setups such as generative adversarial architectures. Thanks to its modular and extensible architecture, KonfAI can easily accommodate custom models, loss functions, and data processing components. The framework has been successfully applied to segmentation, registration, and image synthesis tasks, and has contributed to top-ranking results in several international medical imaging challenges. KonfAI is open source and available at \href{https://github.com/vboussot/KonfAI}{https://github.com/vboussot/KonfAI}.

Segmenting individual instances of mitochondria from imaging datasets can provide rich quantitative information, but is prohibitively time-consuming when done manually, prompting interest in the development of automated algorithms using deep neural networks. Existing solutions for various segmentation tasks are optimized for either: high-resolution three-dimensional imaging, relying on well-defined object boundaries (e.g., whole neuron segmentation in volumetric electron microscopy datasets); or low-resolution two-dimensional imaging, boundary-invariant but poorly suited to large 3D objects (e.g., whole-cell segmentation of light microscopy images). Mitochondria in whole-cell 3D electron microscopy datasets often lie in the middle ground - large, yet with ambiguous borders, challenging current segmentation tools. To address this, we developed skeleton-oriented object segmentation (SKOOTS) - a novel approach that efficiently segments large, densely packed mitochondria. SKOOTS accurately and efficiently segments mitochondria in previously difficult contexts and can also be applied to segment other objects in 3D light microscopy datasets. This approach bridges a critical gap between existing segmentation approaches, improving the utility of automated analysis of three-dimensional biomedical imaging data. We demonstrate the utility of SKOOTS by applying it to segment over 15,000 cochlear hair cell mitochondria across experimental conditions in under 2 hours on a consumer-grade PC, enabling downstream morphological analysis that revealed subtle structural changes following aminoglycoside exposure - differences not detectable using analysis approaches currently used in the field.

A detailed understanding of material structure across multiple scales is essential for predictive modeling of textile-reinforced composites. Nesting -- characterized by the interlocking of adjacent fabric layers through local interpenetration and misalignment of yarns -- plays a critical role in defining mechanical properties such as stiffness, permeability, and damage tolerance. This study presents a framework to quantify nesting behavior in dry textile reinforcements under compaction using low-resolution computed tomography (CT). In-situ compaction experiments were conducted on various stacking configurations, with CT scans acquired at 20.22 $\mu$m per voxel resolution. A tailored 3D{-}UNet enabled semantic segmentation of matrix, weft, and fill phases across compaction stages corresponding to fiber volume contents of 50--60 %. The model achieved a minimum mean Intersection-over-Union of 0.822 and an $F1$ score of 0.902. Spatial structure was subsequently analyzed using the two-point correlation function $S_2$, allowing for probabilistic extraction of average layer thickness and nesting degree. The results show strong agreement with micrograph-based validation. This methodology provides a robust approach for extracting key geometrical features from industrially relevant CT data and establishes a foundation for reverse modeling and descriptor-based structural analysis of composite preforms.

Prevalent knee osteoarthritis (OA) imposes substantial burden on health systems with no cure available. Its ultimate treatment is total knee replacement (TKR). Complications from surgery and recovery are difficult to predict in advance, and numerous factors may affect them. Radiographic knee alignment is one of the key factors that impacts TKR outcomes, affecting outcomes such as postoperative pain or function. Recently, artificial intelligence (AI) has been introduced to the automatic analysis of knee radiographs, for example, to automate knee alignment measurements. Existing review articles tend to focus on knee OA diagnosis and segmentation of bones or cartilages in MRI rather than exploring knee alignment biomarkers for TKR outcomes and their assessment. In this review, we first examine the current scoring protocols for evaluating TKR outcomes and potential knee alignment biomarkers associated with these outcomes. We then discuss existing AI-based approaches for generating knee alignment biomarkers from knee radiographs, and explore future directions for knee alignment assessment and TKR outcome prediction.

Tractography algorithms leverage diffusion MRI to reconstruct the fibrous architecture of the brain's white matter. Among machine learning approaches, reinforcement learning (RL) has emerged as a promising framework for tractography, outperforming traditional methods in several key aspects. TractOracle-RL, a recent RL-based approach, reduces false positives by incorporating anatomical priors into the training process via a reward-based mechanism. In this paper, we investigate four extensions of the original TractOracle-RL framework by integrating recent advances in RL, and we evaluate their performance across five diverse diffusion MRI datasets. Results demonstrate that combining an oracle with the RL framework consistently leads to robust and reliable tractography, regardless of the specific method or dataset used. We also introduce a novel RL training scheme called Iterative Reward Training (IRT), inspired by the Reinforcement Learning from Human Feedback (RLHF) paradigm. Instead of relying on human input, IRT leverages bundle filtering methods to iteratively refine the oracle's guidance throughout training. Experimental results show that RL methods trained with oracle feedback significantly outperform widely used tractography techniques in terms of accuracy and anatomical validity.