arXiv subjects

Artur Yakimovich

Publications and source records attributed to Artur Yakimovich.

12 recordsLinked to original sources

arXiv2026

Noise-Robust Conditional Flow Matching: Generating Clean Samples from Noisy Datasets

Generative models learn the statistical properties of their training data, so high-quality generation depends on clean and representative datasets. In scientific imaging, acquisition often yields noisy measurements, while collecting clean references can be costly, impractical or even unattainable. Training directly on these measurements results in a model that reproduces the corrupted data. This can be circumvented by learning the clean population distribution directly from the noisy data. Conditional flow matching (CFM) combines a simple regression objective with stable training, efficient sampling, and strong image-generation performance, making it a natural framework for this setting. We introduce Noise-Robust Conditional Flow Matching (NR-CFM), an unconditional generator that learns from one corrupted observation per image. NR-CFM provides a closed-form clean endpoint correction for additive white Gaussian noise and learns a data-driven correction for general Gaussian corruptions with more complex covariance structure. Across the evaluated corruption settings, NR-CFM outperforms NR-GAN in most cases and remains competitive with Ambient Diffusion in the high-noise regime. We further evaluate NR-CFM on scientific data at signal-to-noise ratios as low as $0.001$, where it generates plausible particle images from severely corrupted measurements.

cs.CV↗

arXiv2026

Metric-Guided Synthetic Image Data Rendering for Deep Learning compatible with Agentic AI

Deep learning computer vision for scientific applications requires collecting and annotating large datasets in a laborious, expensive and error-prone process. Synthetic data generation through 3D modelling and rendering may simplify this process and increase the accuracy of annotations by generating them programmatically. However, minimising the domain gap between real and synthetic images visually is subjective and lacks systematic quantitative guidance. We present GraNatPy, a Python package with metrics to guide improvement of the rendered scene. We show that quantifiable increase in realism, diversity and size of rendered dataset correlates with improved visual perception of the scene and higher zero-shot performance of an object detection model. Furthermore, we demonstrated using photographs of virological plaque assays that gradient similarity affects performance on small object detection, which can be improved by mixing real and synthetic data. Finally, we turn procedural data rendering into an agentic skill (SynthClaw) to automate the procedural parameter optimisation.

cs.CV↗

arXiv2026

Cryo-SWAN: the Multi-Scale Wavelet-decomposition-inspired Autoencoder Network for molecular density representation of molecular volumes

Learning robust representations of 3D shapes from voxelized data is essential for advancing AI methods in biomedical imaging. However, most contemporary 3D computer vision approaches operate on point clouds, meshes, or octrees, while volumetric density maps, the native format of structural biology and cryo-EM, remain comparatively underexplored. We present Cryo-SWAN, a voxel-based variational autoencoder inspired by multi-scale wavelet decomposition. The model performs conditional coarse-to-fine latent encoding and recursive residual quantization across perception scales, enabling accurate capture of both global geometry and high-frequency structural detail in molecular density volumes. Evaluated on ModelNet40, BuildingNet, and a newly curated dataset of cryo-EM volumes, ProteinNet3D, Cryo-SWAN consistently improves reconstruction quality over state-of-the-art 3D autoencoders. We demonstrate that the molecular densities organize in learned latent space according to shared geometric features, while integration with diffusion models enables denoising and conditional shape generation. Together, Cryo-SWAN is a practical framework for data-driven structural biology and volumetric imaging.

eess.IV↗

arXiv2025

Single-shot Star-convex Polygon-based Instance Segmentation for Spatially-correlated Biomedical Objects

Biomedical images often contain objects known to be spatially correlated or nested due to their inherent properties, leading to semantic relations. Examples include cell nuclei being nested within eukaryotic cells and colonies growing exclusively within their culture dishes. While these semantic relations bear key importance, detection tasks are often formulated independently, requiring multi-shot analysis pipelines. Importantly, spatial correlation could constitute a fundamental prior facilitating learning of more meaningful representations for tasks like instance segmentation. This knowledge has, thus far, not been utilised by the biomedical computer vision community. We argue that the instance segmentation of two or more categories of objects can be achieved in parallel. We achieve this via two architectures HydraStarDist (HSD) and the novel (HSD-WBR) based on the widely-used StarDist (SD), to take advantage of the star-convexity of our target objects. HSD and HSD-WBR are constructed to be capable of incorporating their interactions as constraints into account. HSD implicitly incorporates spatial correlation priors based on object interaction through a joint encoder. HSD-WBR further enforces the prior in a regularisation layer with the penalty we proposed named Within Boundary Regularisation Penalty (WBR). Both architectures achieve nested instance segmentation in a single shot. We demonstrate their competitiveness based on $IoU_R$ and AP and superiority in a new, task-relevant criteria, Joint TP rate (JTPR) compared to their baseline SD and Cellpose. Our approach can be further modified to capture partial-inclusion/-exclusion in multi-object interactions in fluorescent or brightfield microscopy or digital imaging. Finally, our strategy suggests gains by making this learning single-shot and computationally efficient.

cs.CV↗

arXiv2024

Single Exposure Quantitative Phase Imaging with a Conventional Microscope using Diffusion Models

Phase imaging is gaining importance due to its applications in fields like biomedical imaging and material characterization. In biomedical applications, it can provide quantitative information missing in label-free microscopy modalities. One of the most prominent methods in phase quantification is the Transport-of-Intensity Equation (TIE). TIE often requires multiple acquisitions at different defocus distances, which is not always feasible in a clinical setting. To address this issue, we propose to use chromatic aberrations to induce the required through-focus images with a single exposure, effectively generating a through-focus stack. Since the defocus distance induced by the aberrations is small, conventional TIE solvers are insufficient to address the resulting artifacts. We propose Zero-Mean Diffusion, a modified version of diffusion models designed for quantitative image prediction, and train it with synthetic data to ensure robust phase retrieval. Our contributions offer an alternative TIE approach that leverages chromatic aberrations, achieving accurate single-exposure phase measurement with white light and thus improving the efficiency of phase imaging. Moreover, we present a new class of diffusion models that are well-suited for quantitative data and have a sound theoretical basis. To validate our approach, we employ a widespread brightfield microscope equipped with a commercially available color camera. We apply our model to clinical microscopy of patients' urine, obtaining accurate phase measurements.

eess.IV↗

arXiv2024

Heterogeneity of tumor biophysical properties and their potential role as prognostic markers

Progress in our knowledge of tumor mechanisms and complexity led to the understanding of the physical parameters of cancer cells and their microenvironment, including the mechanical, thermal, and electrical properties, solid stress, and liquid pressure, as critical regulators of tumor progression and potential prognostic traits associated with clinical outcomes. The biological hallmarks of cancer and physical abnormalities of tumors are mutually reinforced, promoting a vicious cycle of tumor progression. A comprehensive analysis of the biological and physical tumor parameters is critical for developing more robust prognostic and diagnostic markers and improving treatment efficiency. Like the biological tumor traits, physical tumor features are characterized by inter-and intratumoral heterogeneity. The dynamic changes of physical tumor traits during tumor progression and as a result of tumor treatment highlight the necessity of their spatial and temporal analysis in clinical settings. This review focuses on the biological basis of the tumor-specific physical traits, the state-of-the-art methods of their analyses, and the perspective of clinical translation. The importance of tumor physical parameters for disease progression and therapy resistance, as well as current treatment strategies to monitor and target tumor physical traits in clinics, is highlighted.

physics.bio-ph↗

arXiv2024

Solving the inverse problem of microscopy deconvolution with a residual Beylkin-Coifman-Rokhlin neural network

Optic deconvolution in light microscopy (LM) refers to recovering the object details from images, revealing the ground truth of samples. Traditional explicit methods in LM rely on the point spread function (PSF) during image acquisition. Yet, these approaches often fall short due to inaccurate PSF models and noise artifacts, hampering the overall restoration quality. In this paper, we approached the optic deconvolution as an inverse problem. Motivated by the nonstandard-form compression scheme introduced by Beylkin, Coifman, and Rokhlin (BCR), we proposed an innovative physics-informed neural network Multi-Stage Residual-BCR Net (m-rBCR) to approximate the optic deconvolution. We validated the m-rBCR model on four microscopy datasets - two simulated microscopy datasets from ImageNet and BioSR, real dSTORM microscopy images, and real widefield microscopy images. In contrast to the explicit deconvolution methods (e.g. Richardson-Lucy) and other state-of-the-art NN models (U-Net, DDPM, CARE, DnCNN, ESRGAN, RCAN, Noise2Noise, MPRNet, and MIMO-U-Net), the m-rBCR model demonstrates superior performance to other candidates by PSNR and SSIM in two real microscopy datasets and the simulated BioSR dataset. In the simulated ImageNet dataset, m-rBCR ranks the second-best place (right after MIMO-U-Net). With the backbone from the optical physics, m-rBCR exploits the trainable parameters with better performances (from ~30 times fewer than the benchmark MIMO-U-Net to ~210 times than ESRGAN). This enables m-rBCR to achieve a shorter runtime (from ~3 times faster than MIMO-U-Net to ~300 times faster than DDPM). To summarize, by leveraging physics constraints our model reduced potentially redundant parameters significantly in expertise-oriented NN candidates and achieved high efficiency with superior performance.

q-bio.QM↗

arXiv2024

Conditional Variational Diffusion Models

Inverse problems aim to determine parameters from observations, a crucial task in engineering and science. Lately, generative models, especially diffusion models, have gained popularity in this area for their ability to produce realistic solutions and their good mathematical properties. Despite their success, an important drawback of diffusion models is their sensitivity to the choice of variance schedule, which controls the dynamics of the diffusion process. Fine-tuning this schedule for specific applications is crucial but time-costly and does not guarantee an optimal result. We propose a novel approach for learning the schedule as part of the training process. Our method supports probabilistic conditioning on data, provides high-quality solutions, and is flexible, proving able to adapt to different applications with minimum overhead. This approach is tested in two unrelated inverse problems: super-resolution microscopy and quantitative phase imaging, yielding comparable or superior results to previous methods and fine-tuned diffusion models. We conclude that fine-tuning the schedule by experimentation should be avoided because it can be learned during training in a stable way that yields better results.

cs.CV↗

arXiv2023

Phenotype-preserving metric design for high-content image reconstruction by generative inpainting

In the past decades, automated high-content microscopy demonstrated its ability to deliver large quantities of image-based data powering the versatility of phenotypic drug screening and systems biology applications. However, as the sizes of image-based datasets grew, it became infeasible for humans to control, avoid and overcome the presence of imaging and sample preparation artefacts in the images. While novel techniques like machine learning and deep learning may address these shortcomings through generative image inpainting, when applied to sensitive research data this may come at the cost of undesired image manipulation. Undesired manipulation may be caused by phenomena such as neural hallucinations, to which some artificial neural networks are prone. To address this, here we evaluate the state-of-the-art inpainting methods for image restoration in a high-content fluorescence microscopy dataset of cultured cells with labelled nuclei. We show that architectures like DeepFill V2 and Edge Connect can faithfully restore microscopy images upon fine-tuning with relatively little data. Our results demonstrate that the area of the region to be restored is of higher importance than shape. Furthermore, to control for the quality of restoration, we propose a novel phenotype-preserving metric design strategy. In this strategy, the size and count of the restored biological phenotypes like cell nuclei are quantified to penalise undesirable manipulation. We argue that the design principles of our approach may also generalise to other applications.

eess.IV↗

arXiv2023

Microscopy image reconstruction with physics-informed denoising diffusion probabilistic model

Light microscopy is a widespread and inexpensive imaging technique facilitating biomedical discovery and diagnostics. However, light diffraction barrier and imperfections in optics limit the level of detail of the acquired images. The details lost can be reconstructed among others by deep learning models. Yet, deep learning models are prone to introduce artefacts and hallucinations into the reconstruction. Recent state-of-the-art image synthesis models like the denoising diffusion probabilistic models (DDPMs) are no exception to this. We propose to address this by incorporating the physical problem of microscopy image formation into the model's loss function. To overcome the lack of microscopy data, we train this model with synthetic data. We simulate the effects of the microscope optics through the theoretical point spread function and varying the noise levels to obtain synthetic data. Furthermore, we incorporate the physical model of a light microscope into the reverse process of a conditioned DDPM proposing a physics-informed DDPM (PI-DDPM). We show consistent improvement and artefact reductions when compared to model-based methods, deep-learning regression methods and regular conditioned DDPMs.

q-bio.QM↗

arXiv2023

Roadmap on Deep Learning for Microscopy

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

physics.optics↗

arXiv2017

MatlabCompat.jl: helping Julia understand Your Matlab/Octave Code

Scientific legacy code in MATLAB/Octave not compatible with modernization of research workflows is vastly abundant throughout academic community. Performance of non-vectorized code written in MATLAB/Octave represents a major burden. A new programming language for technical computing Julia, promises to address these issues. Although Julia syntax is similar to MATLAB/Octave, porting code to Julia may be cumbersome for researchers. Here we present MatlabCompat.jl - a library aimed at simplifying the conversion of your MATLAB/Octave code to Julia. We show using a simplistic image analysis use case that MATLAB/Octave code can be easily ported to high performant Julia using MatlabCompat.jl.

cs.SE↗