Papers for
microscopy imaging engineers
Papers whose findings have a practical use for this group, as judged from the abstract. Open a paper to read what it means in practice.
Bmnd improves denoising for scientific data across all dimensions
BMND: Direct Poisson Denoising by N-Dimensional Block Matching and Collaborative Filtering
Abstract: Poisson denoising of scientific data requires methods that account for signal-dependent noise while accommodating different data dimensionalities and preserving quantitative intensity information. We present BMND, a dimension-independent extension of block matching and collaborative filtering for Gaussian and Poisson observations. Building on the two-stage structure of BM3D and BM4D, BMND processes Poisson data directly, without a variance-stabilizing transform, by combining noise-aware patch matching with propagation of signal-dependent noise variances through collaborative filtering and aggregation. A dimension-independent reference-patch traversal scheme supports arrays with an arbitrary number of axes. An optional aggregation-aware mass conservation preserves the observed total intensity after weighted overlap-add. We evaluate the framework on one-dimensional physiological signals, two-dimensional images, and three-dimensional volumes, using controlled noise experiments and measured fluorescence microscopy acquisitions. The experiments demonstrate improved reconstruction quality from noise-aware matching and Wiener filtering, while low-count phantom experiments show reduced denoising-induced intensity loss through mass conservation. The framework provides a unified, non-learning-based approach to denoising across arbitrary data dimensions and is released as an open-source library.
Directional total variation method improves image super-resolution quality
Directional Total Variation-Regularized Implicit Neural Representations (DTV-INR) for Continuous Super-Resolution in Degraded Imaging Domains
Abstract: In this paper, we introduce the Directional Total Variation-Regularized Implicit Neural Representation (DTV-INR), an advanced variational paradigm that synergistically integrates coordinate-driven implicit neural networks with an anisotropic, structure-tensor-informed total variation regularizer tailored for resolution-agnostic image super-resolution. Casting the continuous-to-discrete acquisition process into an ill-posed inverse problem framework, our formulation equips a SIREN-architected coordinate network with a dynamic Riemannian metric tensor field D(x). By leveraging its spectral decomposition, the proposed regularizer preferentially directs diffusion parallel to dominant structural contours while penalizing cross-edge dissipation, successfully circumventing the classical staircasing artifacts inherent to scalar total variation schemes. We rigorously prove the well-posedness of this formulation in H^1(Omega) by establishing the existence, uniqueness, and metric stability of the variational minimizer, and realize this via an alternating projected optimization algorithm that decouples network parameter tuning from adaptive tensor field updates. Comprehensive experiments conducted on clinical brain magnetic resonance imaging (MRI) and biomedical transmission electron microscopy confirm substantial quantitative and qualitative improvements, yielding PSNR enhancements reaching +5.05 dB over baseline unregularized INRs and +1.71-2.85 dB over isotropic TV-INR across continuous (non-integer) upsampling factors, alongside remarkable noise robustness up to sigma_eta = 0.10 and monotonic preconditioned convergence behavior.