BMND: Direct Poisson Denoising by N-Dimensional Block Matching and Collaborative Filtering
Organizations: University of Münster
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.
Figures & tables
| Problem and existing limitations | bmnd approach |
|---|---|
| Different data modalities and noise models. Parameters, dimensions, and noise assumptions are tightly coupled in existing implementations, which limits their reuse across imaging modalities and acquisition settings. | A common formulation with configurable profiles for geometry, noise, matching, shrinkage, and aggregation. |
| Signal-dependent Poisson noise. Standard squared Euclidean block matching and fixed-variance shrinkage are designed for data-independent, stationary Gaussian noise and do not account for the signal dependence of Poisson noise. | Direct scaled-Poisson processing with a plug-in variance map and Poisson-aware matching metrics. |
| Correlated or heteroscedastic noise. A single scalar variance per coefficient is inadequate for nonstationary or correlated noise. | A common covariance interface that propagates noise through transforms, thresholds, Wiener gains, and aggregation weights. |
| Arbitrary-dimensional data. bm3d and bm4d are formulated for specific data dimensionalities and therefore require dimension-dependent implementations of patch extraction, grouping, transforms, and traversal. | Coupled reference-patch schedules and group transforms for arrays with an arbitrary number of data axes. |
| Low-count measurements. High-count asymptotics for discrepancy moments become inaccurate for small pooled counts. | Exact finite-count conditional moments for calibrating acceptance rules and matching scales. |
| Noise-aware block matching. Raw ssd ( ssd ) includes the expected contribution of noise and does not distinguish structural mismatch from noise fluctuations. | Poisson deviance, Pearson and Anscombe discrepancies, and noise-bias-corrected ssd under Gaussian or Poisson models. |
| Method | Metric | |||||
|---|---|---|---|---|---|---|
| Reported by Zhang et al. [ 51 ] | ||||||
| Raw | PSNR (dB) | |||||
| SSIM | ||||||
| VST + BM3D | PSNR (dB) | |||||
| SSIM | ||||||
| PURE-LET | PSNR (dB) | |||||
| Method | 0 dB | 6 dB | 12 dB | 18 dB |
|---|---|---|---|---|
| QRS RMSE | ||||
| BMND | ||||
| Wavelet | ||||
| NLM | ||||
| SSCF | ||||
| Savitzky–Golay | ||||
Appendix figures & tables9 assets
Supplementary material from the paper’s appendix.
Appendix
| Parameter | Stage | BM3D | BM4D |
|---|---|---|---|
| General and scheduling | |||
| Reference schedule | Both | generated | generated |
| Shift density | Both | 2.0 | 2.0 |
| Schedule density | Both | 2 | 2 |
| Covariance and matching | |||
| Local-variance domain | Both | ||
| Profile parameter | Candidate values or fixed setting | Levels |
|---|---|---|
| Varied Cartesian factors | ||
| HT matching distance / policy | poisson_deviance / fixed , poisson_deviance / reference_finite_count , poisson_deviance / candidate_standardized , pearson / fixed , pearson / reference_finite_count , pearson / candidate_standardized , anscombe_ssd / fixed , anscombe_ssd / reference_finite_count , anscombe_ssd / candidate_standardized , ssd / fixed | 10 |
| Exact covariance planes | 4 | |
| Wiener gain | classic , noise-floor , variance-scaled | 3 |
| HT aggregation-weight model | classic , variance | 2 |
| HT aggregation-weight domain | coefficient , windowed_synthesis | 2 |
| Method and parameter | Candidate values or fixed setting | Candidates |
|---|---|---|
| 1D BMND | 240 | |
| Patch length | samples | |
| Reference step | samples | |
| One-sided search radius | ||
| Maximum group size | ||
| Matching-threshold scale |