BMND: Direct Poisson Denoising by N-Dimensional Block Matching and Collaborative Filtering
Christof Duhme, Lars Schiefelbein, Florian Büther, Xiaoyi Jiang
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.