A Zero-Shot Deep Image Prior Framework for Denoising and Deconvolution in Fluorescence Microscopy

Convolutional Neural Networks (CNNs) achieve strong denoising performance by exploiting spatial context from neighboring pixels. Deep Image Prior (DIP) leverages this property to restore images from a single noisy input without requiring large datasets. However, the over-parameterized architecture of DIP often leads to noise fitting during optimization. In this paper, we propose Pool-DIP, a convolution-free architecture that incorporates pooling-based contrast modeling to capture spatial context efficiently. Pool-DIP improves denoising performance while significantly reducing the number of parameters and computational complexity compared to convolution-based DIP models. Experimental results show that Pool-DIP achieves competitive performance across multiple datasets, including a real-world benchmark. Spectral analysis further reveals that Pool-DIP stabilizes the evolution of high-frequency components during optimization and suppresses erroneous high-frequency signals. The proposed architecture also generalizes well to other image restoration tasks such as super-resolution and inpainting.

Recently, Deep Image Prior (DIP) has demonstrated strong capabilities for solving inverse imaging problems (IIPs) by optimizing a randomly initialized convolutional neural network in a training-data-free regime. However, DIP suffers from overfitting to noisy measurements due to network over-parameterization, making early stopping (ES) essential. The most successful ES method tracks fluctuations in the running variance of the network output to detect overfitting. However, in many applications, these fluctuations may appear prematurely, leading to unstable reconstructions. In this paper, we first show that nearly optimal DIP early stopping can be achieved when two independent noisy copies of the degraded image are available. Motivated by this observation, and since obtaining two fully independent copies is infeasible, we propose an overfitting detection framework based on constructing pseudo self-referenced images, resulting in three IIP-specific algorithms. Our approach is further supported by theoretical results on single-reference validation, pseudo-validation estimation, and the impact of shared noise. Across different IIPs, ranging from natural image restoration to medical image reconstruction, and under varying noise levels and noise types, our methods consistently outperform existing DIP early stopping approaches, all without requiring an accurate estimate of the noise level.

Image Scanning Microscopy (ISM) is a fluorescence imaging technique that combines detector-array acquisition and computational reconstruction to achieve the theoretical resolution of an ideal confocal microscope, i.e., one operating with an infinitesimally small pinhole, while maintaining high signal-to-noise ratio. Among the reconstruction methods for obtaining the super-resolved image, multi-image deconvolution (MID) and its extension aimed at preserving the optical sectioning capability of confocal microscopy, known as super-resolution sectioning ISM (s$^2$ISM), are among the most widely used approaches. Both methods rely on Richardson--Lucy-type iterative schemes, whose semi-convergent behavior requires early stopping and often leads to noise amplification and reconstruction artifacts. In this work, we introduce a self-tuning explicit regularization framework for both MID and s$^2$ISM reconstruction. Within a Bayesian maximum a posteriori formulation, we combine a multi-frame Poisson data fidelity term with explicit regularization, considering $\ell_1$ and smoothed total variation penalties as representative examples. We further develop an automatic and ground-truth-free strategy for regularization parameter selection by adapting the residual whiteness principle to the multi-frame Poisson setting and introducing a spectral high-pass extension tailored to s$^2$ISM. The resulting framework enables stable reconstructions without empirical stopping rules. To demonstrate the proposed framework, we consider first-order optimization schemes based on proximal gradient and mirror descent methods with adaptive backtracking strategies. Experiments on simulated and real fluorescence ISM datasets demonstrate improved reconstruction stability and image quality with respect to unregularized approaches, while enabling robust super-resolution and optical sectioning in low-photon conditions.