Computational Cannula Microscopy is a minimally invasive imaging technique that can enable high-resolution imaging deep inside tissue. Here, we apply artificial neural networks to enable fast, power-efficient image reconstructions that are more efficiently scalable to larger fields of view. Specifically, we demonstrate widefield fluorescence microscopy of cultured neurons and fluorescent beads with field of view of 200$μ$m (diameter) and resolution of less than 10$μ$m using a cannula of diameter of only 220$μ$m. In addition, we show that this approach can also be extended to macro-photography.
Computational Cannula Microscopy (CCM) is a high-resolution widefield fluorescence imaging approach deep inside tissue, which is minimally invasive. Rather than using conventional lenses, a surgical cannula acts as a lightpipe for both excitation and fluorescence emission, where computational methods are used for image visualization. Here, we enhance CCM with artificial neural networks to enable 3D imaging of cultured neurons and fluorescent beads, the latter inside a volumetric phantom. We experimentally demonstrate transverse resolution of ~6um, field of view ~200um and axial sectioning of ~…
University of Cambridge（剑桥大学）；Imperial College London（伦敦帝国理工学院）
Understanding how networks of neurons process information is one of the key challenges in modern neuroscience. A necessary step to achieve this goal is to be able to observe the dynamics of large populations of neurons over a large area of the brain. Light-field microscopy (LFM), a type of scanless microscope, is a particularly attractive candidate for high-speed three-dimensional (3D) imaging. It captures volumetric information in a single snapshot, allowing volumetric imaging at video frame-rates. Specific features of imaging neuronal activity using LFM call for the development of novel mach…
Light-field microscopes are able to capture spatial and angular information of incident light rays. This allows reconstructing 3D locations of neurons from a single snap-shot.In this work, we propose a model-inspired deep learning approach to perform fast and robust 3D localization of sources using light-field microscopy images. This is achieved by developing a deep network that efficiently solves a convolutional sparse coding (CSC) problem to map Epipolar Plane Images (EPI) to corresponding sparse codes. The network architecture is designed systematically by unrolling the convolutional Iterat…
Tel Aviv University（特拉维夫大学）；Facebook AI Research（脸书人工智能研究院）
Recently developed methods for rapid continuous volumetric two-photon microscopy facilitate the observation of neuronal activity in hundreds of individual neurons and changes in blood flow in adjacent blood vessels across a large volume of living brain at unprecedented spatio-temporal resolution. However, the high imaging rate necessitates fully automated image analysis, whereas tissue turbidity and photo-toxicity limitations lead to extremely sparse and noisy imagery. In this work, we extend a recently proposed deep learning volumetric blood vessel segmentation network, such that it supports …
Functional optical imaging in neuroscience is rapidly growing with the development of new optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. In this review, we cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.
Harvard University（哈佛大学）；Harvard Medical School（哈佛医学院）；Boston Children’s Hospital（波士顿儿童医院）；ESRF, The European Synchrotron（欧洲同步辐射装置）
Comprehensive, synapse-resolution imaging of the brain will be crucial for understanding neuronal computations and function. In connectomics, this has been the sole purview of volume electron microscopy (EM), which entails an excruciatingly difficult process because it requires cutting tissue into many thin, fragile slices that then need to be imaged, aligned, and reconstructed. Unlike EM, hard X-ray imaging is compatible with thick tissues, eliminating the need for thin sectioning, and delivering fast acquisition, intrinsic alignment, and isotropic resolution. Unfortunately, current state-of-…
Today the gold standard for in vivo imaging through scattering tissue is the point-scanning two-photon microscope (PSTPM). Especially in neuroscience, PSTPM is widely used for deep-tissue imaging in the brain. However, due to sequential scanning, PSTPM is slow. Temporal focusing microscopy (TFM), on the other hand, focuses femtosecond pulsed laser light temporally, while keeping wide-field illumination, and is consequently much faster. However, due to the use of a camera detector, TFM suffers from the scattering of emission photons. As a result, TFM produces images of poor spatial resolution a…
Department of Electrical Engineering, University of Notre Dame（圣母大学电气工程系）；Department of Biological Sciences, University of Notre Dame（圣母大学生物科学系）
Fluorescence microscopy has been a significant tool to observe long-term imaging of embryos (in vivo) growth over time. However, cumulative exposure is phototoxic to such sensitive live samples. While techniques like light-sheet fluorescence microscopy (LSFM) allow for reduced exposure, it is not well suited for deep imaging models. Other computational techniques are computationally expensive and often lack restoration quality. To address this challenge, one can use various low-dosage imaging techniques that are developed to achieve the 3D volume reconstruction using a few slices in the axial …
Primary neuronal cultures have been widely used to study neuronal morphology, neurophysiology, neurodegenerative processes, and molecular mechanism of synaptic plasticity underlying learning and memory. Yet, the unique behavioral properties of neurons make them challenging to study - with phenotypic differences expressed as subtle changes in neuronal arborization rather than easy to assay features such as cell count. The need to analyze morphology, growth, and intracellular transport has motivated the development of increasingly sophisticated microscopes and image analysis techniques. Due to i…
Enhanced Confocal Laser Scanning Microscopy with Adaptive Physics Informed Deep Autoencoders
Georgia State University（佐治亚州立大学）；Riphah International University（里法国际大学）；Roots IVY（鲁茨艾维）；Arid Agriculture University（干旱农业大学）；University of Central Florida（中佛罗里达大学）
