Abstract
Computational image enhancement for microscopy facilitates cutting-edge biological discovery. While promising, the commonly used deep learning methods are computationally expensive owing to the use of general-purpose architectures, which are inefficient for microscopy data. Here, we propose a sparsity-efficient neural network for image enhancement as a deep representation learning solution to inverse problems in imaging. To maximize accessibility, we developed a framework named DeBCR, consisting of a modular Python library and a user-friendly point-and-click DeBCR plugin for Napari, a popular bioimage analysis tool. We provide a detailed protocol for using the DeBCR as a library and a plugin, including data preparation, training, and inference. We compare the image restoration performance of DeBCR to ten current state-of-the-art models over four publicly available datasets spanning crucial modalities in advanced light microscopy. DeBCR demonstrates more robust performance in denoising and deconvolution tasks across all assessed microscopy modalities while requiring notably fewer parameters than existing models.