DeepSTORM3D: dense three dimensional localization microscopy and point spread function design by deep learning

Localization microscopy is an imaging technique in which the positions of individual nanoscale point emitters (e.g. fluorescent molecules) are determined at high precision from their images. This is the key ingredient in single/multiple-particle-tracking and several super-resolution microscopy approaches. Localization in three-dimensions (3D) can be performed by modifying the image that a point-source creates on the camera, namely, the point-spread function (PSF). The PSF is engineered using additional optical elements to vary distinctively with the depth of the point-source. However, localizing multiple adjacent emitters in 3D poses a significant algorithmic challenge, due to the lateral overlap of their PSFs. Here, we train a neural network to receive an image containing densely overlapping PSFs of multiple emitters over a large axial range and output a list of their 3D positions. Furthermore, we then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach numerically as well as experimentally by 3D STORM imaging of mitochondria, and volumetric imaging of dozens of fluorescently-labeled telomeres occupying a mammalian nucleus in a single snapshot.Comment: main text: 9 pages, 5 figures, supplementary information: 29 pages, 20 figure

Joint Image and Depth Estimation With Mask-Based Lensless Cameras

Mask-based lensless cameras replace the lens of a conventional camera with a custom mask. These cameras can potentially be very thin and even flexible. Recently, it has been demonstrated that such mask-based cameras can recover light intensity and depth information of a scene. Existing depth recovery algorithms either assume that the scene consists of a small number of depth planes or solve a sparse recovery problem over a large 3D volume. Both these approaches fail to recover the scenes with large depth variations. In this paper, we propose a new approach for depth estimation based on an alternating gradient descent algorithm that jointly estimates a continuous depth map and light distribution of the unknown scene from its lensless measurements. We present simulation results on image and depth reconstruction for a variety of 3D test scenes. A comparison between the proposed algorithm and other method shows that our algorithm is more robust for natural scenes with a large range of depths. We built a prototype lensless camera and present experimental results for reconstruction of intensity and depth maps of different real objects

Thin On-Sensor Nanophotonic Array Cameras

Today's commodity camera systems rely on compound optics to map light originating from the scene to positions on the sensor where it gets recorded as an image. To record images without optical aberrations, i.e., deviations from Gauss' linear model of optics, typical lens systems introduce increasingly complex stacks of optical elements which are responsible for the height of existing commodity cameras. In this work, we investigate flat nanophotonic computational cameras as an alternative that employs an array of skewed lenslets and a learned reconstruction approach. The optical array is embedded on a metasurface that, at 700~nm height, is flat and sits on the sensor cover glass at 2.5~mm focal distance from the sensor. To tackle the highly chromatic response of a metasurface and design the array over the entire sensor, we propose a differentiable optimization method that continuously samples over the visible spectrum and factorizes the optical modulation for different incident fields into individual lenses. We reconstruct a megapixel image from our flat imager with a learned probabilistic reconstruction method that employs a generative diffusion model to sample an implicit prior. To tackle scene-dependent aberrations in broadband, we propose a method for acquiring paired captured training data in varying illumination conditions. We assess the proposed flat camera design in simulation and with an experimental prototype, validating that the method is capable of recovering images from diverse scenes in broadband with a single nanophotonic layer.Comment: 18 pages, 12 figures, to be published in ACM Transactions on Graphic

Analysis of Diffractive Neural Networks for Seeing Through Random Diffusers

Imaging through diffusive media is a challenging problem, where the existing solutions heavily rely on digital computers to reconstruct distorted images. We provide a detailed analysis of a computer-free, all-optical imaging method for seeing through random, unknown phase diffusers using diffractive neural networks, covering different deep learning-based training strategies. By analyzing various diffractive networks designed to image through random diffusers with different correlation lengths, a trade-off between the image reconstruction fidelity and distortion reduction capability of the diffractive network was observed. During its training, random diffusers with a range of correlation lengths were used to improve the diffractive network's generalization performance. Increasing the number of random diffusers used in each epoch reduced the overfitting of the diffractive network's imaging performance to known diffusers. We also demonstrated that the use of additional diffractive layers improved the generalization capability to see through new, random diffusers. Finally, we introduced deliberate misalignments in training to 'vaccinate' the network against random layer-to-layer shifts that might arise due to the imperfect assembly of the diffractive networks. These analyses provide a comprehensive guide in designing diffractive networks to see through random diffusers, which might profoundly impact many fields, such as biomedical imaging, atmospheric physics, and autonomous driving.Comment: 42 Pages, 9 Figure