Samuel J. Yang

Samuel J. Yang
Google Inc. | Google

PhD

About

28
Publications
8,352
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1,867
Citations

Publications

Publications (28)
Article
Full-text available
Phase spatial light modulators (SLMs) are widely used for generating multifocal three-dimensional (3D) illumination patterns, but these are limited to a field of view constrained by the pixel count or size of the SLM. Further, with two-photon SLM-based excitation, increasing the number of focal spots penalizes the total signal linearly - requiring...
Article
Full-text available
Fundamental display characteristics are constantly being improved, especially resolution, dynamic range, and color reproduction. However, whereas high resolution and high-dynamic range displays have matured as a technology, it remains largely unclear how to extend the color gamut of a display without either sacrificing light throughput or making ot...
Article
Full-text available
Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that re...
Article
Full-text available
Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded l...
Article
Full-text available
We report the implementation of a fully on-chip, lensless, sub-pixel resolving optofluidic microscope (SROFM). The device utilizes microfluidic flow to deliver specimens directly across a complementary metal oxide semiconductor (CMOS) sensor to generate a sequence of low-resolution (LR) projection images, where resolution is limited by the sensor's...
Article
Full-text available
Drug discovery for diseases such as Parkinson’s disease are impeded by the lack of screenable cellular phenotypes. We present an unbiased phenotypic profiling platform that combines automated cell culture, high-content imaging, Cell Painting, and deep learning. We applied this platform to primary fibroblasts from 91 Parkinson’s disease patients and...
Article
Full-text available
Significance Automation is accelerating the discovery of useful materials, yet testing even a small fraction of the billions of possible materials for a desired property is beyond the reach of workflows involving resource-intensive property measurements. Due to relationships among composition, structure, and properties, identifying a complex materi...
Preprint
Full-text available
Drug discovery for Parkinson’s disease (PD) is impeded by the lack of screenable phenotypes in scalable cell models. Here we present a novel unbiased phenotypic profiling platform that combines automation, Cell Painting, and deep learning. We applied this platform to primary fibroblasts from 91 PD patients and carefully matched healthy controls, ge...
Preprint
Full-text available
This paper introduces a supervised deep-learning network that jointly optimizes the physical setup of an optical microscope to infer fluorescence image information. Specifically, we design a bright-field microscope's illumination module to maximize the performance for inference of fluorescent cellular features from bright-field imagery. We take adv...
Preprint
Confounding variables are a well known source of nuisance in biomedical studies. They present an even greater challenge when we combine them with black-box machine learning techniques that operate on raw data. This work presents two case studies. In one, we discovered biases arising from systematic errors in the data generation process. In the othe...
Article
Full-text available
The etiological underpinnings of many CNS disorders are not well understood. This is likely due to the fact that individual diseases aggregate numerous pathological subtypes, each associated with a complex landscape of genetic risk factors. To overcome these challenges, researchers are integrating novel data types from numerous patients, including...
Article
Prolonged behavioral challenges can cause animals to switch from active to passive coping strategies to manage effort-expenditure during stress; such normally adaptive behavioral state transitions can become maladaptive in psychiatric disorders such as depression. The underlying neuronal dynamics and brainwide interactions important for passive cop...
Article
Microscopy is a central method in life sciences. Many popular methods, such as antibody labeling, are used to add physical fluorescent labels to specific cellular constituents. However, these approaches have significant drawbacks, including inconsistency; limitations in the number of simultaneous labels because of spectral overlap; and necessary pe...
Article
Full-text available
Background: Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using automated image analysis with high accuracy is important for obtaining a clean, unbiased image dataset. Complicating this task is th...
Article
Full-text available
Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be captured from images, from which similarities between different drugs applied at different dosages can be quantifi...
Article
Full-text available
The successful planning and execution of adaptive behaviors in mammals may require long-range coordination of neural networks throughout cerebral cortex. The neuronal implementation of signals that could orchestrate cortex-wide activity remains unclear. Here, we develop and apply methods for cortex-wide Ca²⁺ imaging in mice performing decision-maki...
Preprint
Tracking the coordinated activity of cellular events through volumes of intact tissue is a major challenge in biology that has inspired significant technological innovation. Yet scanless measurement of the high-speed activity of individual neurons across three dimensions in scattering mammalian tissue remains an open problem. Here we develop and va...
Article
Real-time activity measurements from multiple specific cell populations and projections are likely to be important for understanding the brain as a dynamical system. Here we developed frame-projected independent-fiber photometry (FIP), which we used to record fluorescence activity signals from many brain regions simultaneously in freely behaving mi...
Conference Paper
We both extend the field-of-view and increase the signal in two-photon computer generated holography by using galvanometer mirrors to time-sequentially reposition multiple 3D holograms. We apply this toward 3D two-photon in vivo neuronal calcium imaging.
Article
Full-text available
We report on the implementation of color sub-pixel resolving optofluidic microscope (SROFM), a high resolution (HR) on-chip imaging system for diagnostic applications in rural regions. With the combination of microfluidics and inexpensive complementary metal oxide semiconductor (CMOS) image sensors, we demonstrate optical resolution of 0.66 µm at t...
Conference Paper
We report the implementation of a fully on-chip, lensless, sub-pixel resolving optofluidic microscope (SROFM) based on the super resolution algorithm. The device utilizes microfluidic flow to deliver specimens directly across a complementary metal oxide semiconductor (CMOS) sensor to generate a sequence of low-resolution (LR) projection images, whe...
Conference Paper
The on-chip detection of a weak optical signal in biological experiments can easily be complicated by the presence of an overwhelming background signal, and as such, pre-detection background suppression is substantively important for weak signal detection. In this paper, we report a structure that can be directly incorporated onto optical sensors t...
Article
The on-chip detection of a weak optical signal in biological experiments can easily be complicated by the presence of an overwhelming background signal, and as such, pre-detection background suppression is substantively important for weak signal detection. In this paper, we report a structure that can be directly incorporated onto optical sensors t...
Article
We demonstrate an optofluidic microscopy scheme which can acquire stereo images, utilizing different angles of illumination for projection imaging with our sub-pixel resolving optofluidic microscope.
Article
We report on the implementation of a color-capable sub-pixel resolving optofluidic microscope based on the pixel super-resolution algorithm and sequential RGB illumination, for low-cost on-chip color imaging of biological samples with sub-cellular resolution.

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