Deep-learning-augmented Computational Miniature Mesoscope

Abstract: Fluorescence microscopy is essential to study biological structures and dynamics. However, existing systems suffer from a tradeoff between field-of-view (FOV), resolution, and complexity, and thus cannot fulfill the emerging need of miniaturized platforms providing micron-scale resolution across centimeter-scale FOVs. To overcome this challenge, we developed Computational Miniature Mesoscope (CM$<sup>2$) that exploits a computational imaging strategy to enable single-shot 3D high-resolution imaging across a wide FOV in a miniaturized platform. Here, we present CM$<sup>2$ V2 that significantly advances both the hardware and computation. We complement the 3$\times$3 microlens array with a new hybrid emission filter that improves the imaging contrast by 5$\times$, and design a 3D-printed freeform collimator for the LED illuminator that improves the excitation efficiency by 3$\times$. To enable high-resolution reconstruction across the large imaging volume, we develop an accurate and efficient 3D linear shift-variant (LSV) model that characterizes the spatially varying aberrations. We then train a multi-module deep learning model, CM$<sup>2$Net, using only the 3D-LSV simulator. We show that CM$<sup>2$Net generalizes well to experiments and achieves accurate 3D reconstruction across a $\sim$7-mm FOV and 800-$\mu$m depth, and provides $\sim$6-$\mu$m lateral and $\sim$25-$\mu$m axial resolution. This provides $\sim$8$\times$ better axial localization and $\sim$1400$\times$ faster speed as compared to the previous model-based algorithm. We anticipate this simple and low-cost computational miniature imaging system will be impactful to many large-scale 3D fluorescence imaging applications.