Research Spectrum: Biomedical Imaging Research & Innovation

Automated Morphological Profiling via Deep Learning-Based Segmentation for High-Throughput Phenotypic Screening

Bendegúz H. Zováthi — 2026-08-20

Reproducible morphological profiling, particularly for drug discovery, has become an important tool for compound evaluation. Established workflows such as CellProfiler provide a widely adopted foundation for Cell Painting analysis. However, conventional pipelines often require substantial manual configuration and technical expertise, which can limit scalability and accessibility. In this study, a fully automated deep learning-based workflow is presented for segmentation-driven morphological profiling from raw microscopy data. Using a curated subset of the JUMP Cell Painting pilot dataset, ground-truth masks were generated and used to train a U-net–based segmentation model in the IKOSA platform. Post-processing strategies were introduced to improve instance separation and reduce segmentation artifacts. The final model achieved strong segmentation performance (precision/recall/AP up to 0.98/0.94/0.92 for nuclei), with an average runtime of 2.2 s per 1080 × 1080 image. Segmentation outputs enabled large-scale feature extraction, yielding 3664 morphological descriptors that showed high correlation with CellProfiler-derived measurements (normalized MAE: 0.0298). Feature prioritization further reduced redundancy to 1145 informative descriptors. These results demonstrate that automated deep learning pipelines can complement established Cell Painting workflows by reducing configuration overhead while maintaining compatibility with validated morphological profiling standards. The proposed workflow may help improve resource efficiency in drug discovery and personalized medicine.

Comparative Assessment of Hyperspectral Image Segmentation Algorithms for Fruit Defect Detection Under Different Illumination Conditions

Anastasia Zolotukhina — 2026-08-20

This study presents a comparative analysis of hyperspectral image segmentation algorithms for fruit defect detection under different illumination conditions. The research evaluates the performance of four segmentation methods (Spectral Angle Mapper, Random Forest, Support Vector Machine, and Neural Network) using three distinct illumination modes (local, simultaneous and sequential). The experimental setup employed hyperspectral imaging to assess tomato fruit samples, with data acquisition performed across the 450–850 nm spectral range. Quantitative metrics, including accuracy, error rate, precision, recall, F1-score, and Intersection over Union (IoU), were used to evaluate algorithm performance. Key findings indicate that Random Forest demonstrated superior performance across most metrics, particularly under simultaneous illumination conditions. The highest accuracy was achieved by Random Forest under sequential illumination (0.9971), while the best combination of segmentation metrics was obtained under simultaneous illumination, with an F1-score of 0.8996 and an IoU of 0.8176. The Neural Network showed competitive results. The Spectral Angle Mapper proved sensitive to illumination variations but excelled in specific scenarios requiring minimal memory usage. By demonstrating that acquisition protocol optimization can substantially improve segmentation performance, our results support the development of accurate, non-contact, high-throughput inspection systems and contribute to reducing postharvest losses and improving supply chain quality control.

Influence of Intrapancreatic Fat Deposition on Regional and Total Pancreatic T1 Relaxation Times at 3.0 Tesla MRI

Xiatiguli Shamaitijiang — 2026-08-20

Longitudinal relaxation time (T1) can be used to assess pancreatic pathology on magnetic resonance imaging (MRI). Although pancreatic T1 values may be influenced by intraorgan fat content, regional variation within the pancreas and the impact of potential confounders have not been comprehensively examined. This study aimed to investigate the nuanced associations between intrapancreatic fat deposition (IPFD) and both regional and total pancreatic T1 relaxation times. Pancreatic T1 relaxation times were quantified with B1-corrected dual flip-angle 3D-VIBE imaging at 3.0 Tesla, whereas IPFD was measured with a high-speed, T2-corrected multi-echo sequence. Linear regression models were constructed to evaluate the association between IPFD and T1 values, with adjustment for relevant covariates. A total of 124 individuals were included in the analysis. IPFD explained
4.6% of the variance in total pancreatic T1 values, with notable regional differences: 1.0% in the head, 3.0% in the body, and 7.7% in the tail of the pancreas. In the fully adjusted model, IPFD was significantly associated with total pancreatic T1 values (p = 0.001), with consistent significant associations observed across all pancreatic regions: head (p = 0.03), body (p = 0.004), and tail (p = 0.002). These findings demonstrate that IPFD is a significant determinant of pancreatic T1 relaxation times. Accordingly, IPFD should be considered a potential confounder in pancreatic T1 assessments and accounted for when interpreting T1 relaxation times on pancreatic MRI in both research and clinical contexts.

High-Resolution Measurement of Surface Normal Maps Using Specular Reflection Imaging

Shinichi Inoue — 2026-08-20

This paper presents a method for measuring the spatial distribution of surface normal vectors with high angular accuracy. The measured data are visualized using a color-mapping technique and represented as normal maps, which are commonly used in computer graphics. Reliable methods for evaluating material surface properties have long been sought in industrial applications where visual assessments of reflective properties are still widely employed, particularly in appearance-critical fields. Motivated by this need, we introduce an imaging-based technique for measuring the high-resolution spatial distribution of surface normal vectors from specular reflection. A dedicated measurement apparatus was developed to capture surface normal vectors at 1024 × 1024 sampling points with a spatial resolution of 0.02 × 0.02 mm and an angular resolution of approximately 0.1^◦. Using this
apparatus, normal maps were obtained for various materials, including plastic, ceramic tile, inkjet paper, and aluminum sheets. The spatial distribution of surface normal vectors reflects surface roughness, which strongly influences perceived texture. The resulting normal maps enable not only quantitative surface analysis for industrial inspection but also the physical reproduction of gloss in computer graphics.

Radon-Guided Wavelet-Domain Attention U-Net for Periodic Artifact Suppression in Brain MRI

Jesus David Rios-Perez — 2026-05-21

Periodic artifacts such as ringing (Gibbs), herringbone (spike/corduroy), and zipper patterns degrade the quality of brain MRI. We present a reproducible framework that (i) synthetically generates periodic artifacts with controllable severity directly in k-space, (ii) normalizes pattern orientation through a Radon-guided alignment step, and (iii) corrects them in the wavelet domain using a 2D DWT (AA/AD/DA/DD) with a band-weighted loss. The evaluation was conducted using DLBS T1-weighted 3T MRI volumes with synthetically generated periodic artifacts. It combined global image-quality metrics (SSIM, PSNR) with per-band metrics to quantify how correction concentrates on high-frequency components, and included ablation studies, mixed-artifact stress tests, and structural preservation analyses. Compared with several baseline architectures, the proposed approach shows improvements in structural fidelity and a reduction in periodic patterns (SSIM: 0.985 ± 0.022; PSNR: 43.337 ± 5.364; reduction in concentrated error in high-frequency bands), while preserving unaffected structures. These findings indicate that, within a controlled synthetic benchmark, aligning the pattern orientation prior to learning and optimizing correction in the wavelet domain enables suppression of synthetically generated periodic artifacts while limiting over-smoothing.