50 Years of Image Analysis

The competition between resolution and the imaging field of view is a long-standing problem in traditional imaging systems — they can produce either an image of a small area with fine details or an image of a large area with coarse details. Fourier ptychography (FP) is an approach for tackling this intrinsic trade-off in imaging systems. It takes the challenge of high-throughput and high-resolution imaging from the domain of improving the physical limitations of optics to the domain of computation. It also enables post-measurement computational correction of optical aberrations. We present the basic concept of FP, compare it to related imaging modalities and then discuss experimental implementations, such as aperture-scanning FP, macroscopic camera-scanning FP, reflection mode, single-shot set-up, X-ray FP, speckle-scanning scheme and deep-learning-related implementations. Various applications of FP are discussed, including quantitative phase imaging in 2D and 3D, digital pathology, high-throughput cytometry, aberration metrology, long-range imaging and coherent X-ray nanoscopy. A collection of datasets and reconstruction codes is provided for readers interested in implementing FP themselves. Fourier ptychography is an imaging approach that addresses the intrinsic trade-off between resolution and field of view in optical systems and provides computational correction of optical aberrations. This Technical Review surveys its implementations and applications.

Concept, implementations and applications of Fourier ptychography

Iterative tomography with digital adaptive optics permits hour-long intravital observation of 3D subcellular dynamics at millisecond scale.

Fluorescence microscopes are indispensable to biology and neuroscience. The need for recording in freely behaving animals has further driven the development in miniaturized microscopes (miniscopes). However, conventional microscopes/miniscopes are inherently constrained by their limited space-bandwidth product, shallow depth of field (DOF), and inability to resolve three-dimensional (3D) distributed emitters. Here, we present a Computational Miniature Mesoscope (CM2) that overcomes these bottlenecks and enables single-shot 3D imaging across an 8 mm by 7 mm field of view and 2.5-mm DOF, achieving 7-μm lateral resolution and better than 200-μm axial resolution. The CM2 features a compact lightweight design that integrates a microlens array for imaging and a light-emitting diode array for excitation. Its expanded imaging capability is enabled by computational imaging that augments the optics by algorithms. We experimentally validate the mesoscopic imaging capability on 3D fluorescent samples. We further quantify the effects of scattering and background fluorescence on phantom experiments.

https://advances.sciencemag.org/content/advances/6/43/eabb7508.full.pdf

Single-shot 3D wide-field fluorescence imaging with a Computational Miniature Mesoscope.

Fluorescence imaging of large-scale neural ensemble dynamics

Large-scale imaging of biological dynamics with high spatiotemporal resolution is indispensable to system biology studies However, conventional microscopes have an inherent compromise between the achievable field of view and spatial resolution due to the space–bandwidth product theorem In addition, a further challenge is the ability to handle the enormous amount of data generated by a large-scale imaging platform Here, we break these bottlenecks by proposing the use of a flat–curved–flat imaging strategy, in which the sample plane is magnified onto a large spherical image surface and then seamlessly conjugated to multiple planar sensors Our real-time, ultra-large-scale, high-resolution (RUSH) imaging platform operates with a 10 × 12 mm2 field of view, a uniform resolution of ~120 μm after deconvolution and a data throughput of 51 gigapixels per second We use the RUSH platform to perform video-rate, gigapixel imaging of biological dynamics at centimetre scale and micrometre resolution, including brain-wide structural imaging and functional imaging in awake, behaving mice Video-rate imaging of the brains of awake mice with a field of view of 10 × 12 mm2 and a spatial resolution of 12 µm is accomplished

Video-rate imaging of biological dynamics at centimetre scale and micrometre resolution

https://robots.iopscience.iop.org/article/10.1088/1361-6463/ab946e/pdf

Guofan Jin

Papers

Video-rate imaging of biological dynamics at centimetre scale and micrometre resolution

Advances in point spread function engineering for functional imaging of neural circuits in vivo