The sampling patterns of the light field microscope (LFM) are highly depth-dependent, which implies non-uniform recoverable lateral resolution across depth. Moreover, reconstructions using state-of-the-art approaches suffer from strong artifacts at axial ranges, where the LFM samples the light field at a coarse rate. In this work, we analyze the sampling patterns of the LFM, and introduce a flexible light field point spread function model (LFPSF) to cope with arbitrary LFM designs. We then propose a novel aliasing-aware deconvolution scheme to address the sampling artifacts. We demonstrate the high potential of the proposed method on real experimental data.

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We present a novel deep learning approach to reconstruct confocal microscopy stacks from single light field images. To perform the reconstruction, we introduce the LFMNet, a novel neural network architecture inspired by the U-Net design [1]. It is able to reconstruct with high-accuracy a 112 × 112 × 57.6µm 3 volume (1287 × 1287 × 64 voxels) in 50ms given a single light field image of 1287 × 1287 pixels, thus dramatically reducing 720-fold the time for confocal scanning of assays at the same volumetric resolution and 64-fold the required storage. To prove the applicability in life sciences, our approach is evaluated both quantitatively and qualitatively on mouse brain slices with fluorescently labelled blood vessels. Because of the drastic reduction in scan time and storage space, our setup and method are directly applicable to real-time in vivo 3D microscopy. We provide analysis of the optical design, of the network architecture and of our training procedure to optimally reconstruct volumes for a given target depth range. To train our network, we built a data set of 362 light field images of mouse brain blood vessels and the corresponding aligned set of 3D confocal scans, which we use as ground truth. The data set will be made available for research purposes [2].

We present a novel learning-based method to build a differentiable computational model of a real fluorescence microscope. Our model can be used to calibrate a real optical setup directly from data samples and to engineer point spread functions by specifying the desired input-output data. This approach is poised to drastically improve the design of microscopes, because the parameters of current models of optical setups cannot be easily fit to real data. Inspired by the recent progress in deep learning, our solution is to build a differentiable wave optics simulator as a composition of trainable modules, each computing light wave-front (WF) propagation due to a specific optical element. We call our differentiable modules WaveBlocks and show reconstruction results in the case of lenses, wave propagation in air, camera sensors and diffractive elements (e.g., phase-masks).