Jay Nadeau
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View article: Microbial communities of selected regions of the Deep Springs Lake aquifer system
Microbial communities of selected regions of the Deep Springs Lake aquifer system Open
Deep Springs Lake is a small, isolated, highly alkaline soda lake in Inyo County of Eastern California, USA. It is a seasonally filled salt lake or playa, and is part of a closed aquifer system. Such closed systems are globally rare, occur…
View article: Synthesis and Characterization of Highly Stable Fisetin Encapsulated in Lecithin-Chitosan-Savie Nanoparticles
Synthesis and Characterization of Highly Stable Fisetin Encapsulated in Lecithin-Chitosan-Savie Nanoparticles Open
Senolytic drugs, of the class of polyphenolic flavonoids, have attracted attention for a wide variety of medical applications for which they may be delivered topically, orally, and/or intravenously. However, due to their hydrophobicity and…
View article: Extant life detection using label-free video microscopy in analog aquatic environments
Extant life detection using label-free video microscopy in analog aquatic environments Open
The ability of microbial active motion, morphology, and optical properties to serve as biosignatures was investigated by in situ video microscopy in a wide range of extreme field sites where such imaging had not been performed previously. …
View article: Motion history images: a new method for tracking microswimmers in 3D
Motion history images: a new method for tracking microswimmers in 3D Open
Quantitative tracking of rapidly moving micron-scale objects remains an elusive challenge in microscopy due to low signal-to-noise. This paper describes a novel method for tracking micron-sized motile organisms in off-axis Digital Holograp…
View article: Fluorescence Microscopy with Deep UV, Near UV, and Visible Excitation for <i>In Situ</i> Detection of Microorganisms
Fluorescence Microscopy with Deep UV, Near UV, and Visible Excitation for <i>In Situ</i> Detection of Microorganisms Open
We report a simple, inexpensive design of a fluorescence microscope with light-emitting diode (LED) excitation for detection of labeled and unlabeled microorganisms in mineral substrates. The use of deep UV (DUV) excitation with visible em…
View article: The use of fluorescence lifetime imaging (FLIM) for in situ microbial detection in complex mineral substrates
The use of fluorescence lifetime imaging (FLIM) for in situ microbial detection in complex mineral substrates Open
The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis , and Bacillus subtilis labelled …
View article: Onboard Science Instrument Autonomy for the Detection of MicroscopyBiosignatures on the Ocean Worlds Life Surveyor
Onboard Science Instrument Autonomy for the Detection of MicroscopyBiosignatures on the Ocean Worlds Life Surveyor Open
The quest to find extraterrestrial life is a critical scientific endeavor with civilization-level implications. Icy moons in our solar system are promising targets for exploration because their liquid oceans make them potential habitats fo…
View article: Onboard Science Instrument Autonomy for the Detection of Microscopy Biosignatures on the Ocean Worlds Life Surveyor
Onboard Science Instrument Autonomy for the Detection of Microscopy Biosignatures on the Ocean Worlds Life Surveyor Open
The quest to find extraterrestrial life is a critical scientific endeavor with civilization-level implications. Icy moons in our solar system are promising targets for exploration because their liquid oceans make them potential habitats fo…
View article: Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park
Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park Open
Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection o…
View article: Recent advances in experimental design and data analysis to characterize prokaryotic motility
Recent advances in experimental design and data analysis to characterize prokaryotic motility Open
Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and phy…
View article: Biogeochemical Responses to Mixing of Glacial Meltwater and Hot Spring Discharge in the Mount St. Helens Crater
Biogeochemical Responses to Mixing of Glacial Meltwater and Hot Spring Discharge in the Mount St. Helens Crater Open
Environments where geothermal waters and glacier meltwater mix are common on Earth yet little is known about the biogeochemical processes that occur when hot, reduced geothermal water mixes with cold, oxidized glacial meltwater in natural …
View article: Biogeochemical responses to mixing of glacial meltwater and hot spring discharge in the Mount St. Helens crater
Biogeochemical responses to mixing of glacial meltwater and hot spring discharge in the Mount St. Helens crater Open
Analytical measurements of water at the three sampling sites: glacier, hot spring and downstream. Error in measurements (±) represents 1 standard deviation when replicate laboratory measurements were taken. Limit of detection (LoD) was cal…
View article: A multi-modal volumetric microscope with automated sample handling for surveying microbial life in liquid samples
A multi-modal volumetric microscope with automated sample handling for surveying microbial life in liquid samples Open
In the study of microbial life, microscopy plays a unique role due to its ability to detect ordered structure, motility, and fluorescence signals. As such it has also recently gained attention in the context of searching for extant life on…
View article: Quantification of Motility in Bacillus subtilis at Temperatures Up to 84°C Using a Submersible Volumetric Microscope and Automated Tracking
Quantification of Motility in Bacillus subtilis at Temperatures Up to 84°C Using a Submersible Volumetric Microscope and Automated Tracking Open
We describe a system for high-temperature investigations of bacterial motility using a digital holographic microscope completely submerged in heated water. Temperatures above 90°C could be achieved, with a constant 5°C offset between the s…
View article: Microscopic Object Classification through Passive Motion Observations with Holographic Microscopy
Microscopic Object Classification through Passive Motion Observations with Holographic Microscopy Open
Digital holographic microscopy provides the ability to observe throughout a volume that is large compared to its resolution without the need to actively refocus to capture the entire volume. This enables simultaneous observations of large …
View article: 2D vs 3D tracking in bacterial motility analysis
2D vs 3D tracking in bacterial motility analysis Open
Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fas…
View article: Genetically Encoded Phase Contrast Agents for Digital Holographic Microscopy
Genetically Encoded Phase Contrast Agents for Digital Holographic Microscopy Open
Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure, and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques curre…
View article: Using the Gouy phase anomaly to localize and track bacteria in digital holographic microscopy 4D images
Using the Gouy phase anomaly to localize and track bacteria in digital holographic microscopy 4D images Open
Described over 100 years ago, the Gouy phase anomaly refers to the additional phase shift that is accumulated as a wave passes through focus. It is potentially useful in analyzing any type of phase-sensitive imaging; in light microscopy,…
View article: Characterization of Retinol Stabilized in Phosphatidylcholine Vesicles with and without Antioxidants
Characterization of Retinol Stabilized in Phosphatidylcholine Vesicles with and without Antioxidants Open
Retinol stability has been reported to be improved by encapsulation in liposomes, both with and without cholesterol. However, this improvement is limited because of lipid peroxidation. In this study, we compare the stability of retinol in …
View article: ELVIS: A Correlated Light-Field and Digital Holographic Microscope for Field and Laboratory Investigations – Field Demonstration
ELVIS: A Correlated Light-Field and Digital Holographic Microscope for Field and Laboratory Investigations – Field Demonstration Open
View article: Enhancing final image contrast in off-axis digital holography using residual fringes
Enhancing final image contrast in off-axis digital holography using residual fringes Open
We show that background fringe-pattern subtraction is a useful technique for removing static noise from off-axis holographic reconstructions and can enhance image contrast in volumetric reconstructions by an order of magnitude in the case …
View article: Microscopic Object Classification through Passive Motion Observations with Holographic Microscopy
Microscopic Object Classification through Passive Motion Observations with Holographic Microscopy Open
Digital holographic microscopy provides the ability to observe throughout a volume that is large compared to its resolution element without the need to refocus through the volume. This capability enables simultaneous observations of large …
View article: Supplementary document for Using the Gouy phase anomaly to localize and track bacteria in digital holographic microscopy 4D images - 4880204.pdf
Supplementary document for Using the Gouy phase anomaly to localize and track bacteria in digital holographic microscopy 4D images - 4880204.pdf Open
Supplemental figures and code
View article: Genetically encoded phase contrast agents for digital holographic microscopy
Genetically encoded phase contrast agents for digital holographic microscopy Open
Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques curren…
View article: Large Data Considerations in Digital Holographic Microscopy
Large Data Considerations in Digital Holographic Microscopy Open
Digital holographic microscopy (DHM) is an interferometric technique with several advantages over traditional light microscopy.A hologram is an interference pattern produced by a coherent "reference" beam recombining with an "object" beam …
View article: ELVIS: A Correlated Light-Field and Digital Holographic Microscope for Field and Laboratory Investigations
ELVIS: A Correlated Light-Field and Digital Holographic Microscope for Field and Laboratory Investigations Open
We are developing a unique multi-modal volumetric microscope capable of instantaneous imaging of sample volumes approximately 100-fold larger than those sampled by conventional fluorescence microscopy, with spatial resolution sufficient to…
View article: Multiwavelength Digital Holographic Imaging and Phase Unwrapping of Protozoa Using Custom Fiji Plug-ins
Multiwavelength Digital Holographic Imaging and Phase Unwrapping of Protozoa Using Custom Fiji Plug-ins Open
Multiwavelength digital holographic microscopy (DHM) has been used to improve phase reconstructions of digital holograms by reducing 2π phase ambiguities. However, most samples used as test images have been solid or adhered to a surface, m…
View article: A machine learning algorithm for identifying and tracking bacteria in three dimensions using Digital Holographic Microscopy
A machine learning algorithm for identifying and tracking bacteria in three dimensions using Digital Holographic Microscopy Open
Digital Holographic Microscopy (DHM) is an emerging technique for three-dimensional imaging of microorganisms due to its high throughput and large depth of field relative to traditional microscopy techniques. While it has shown substantial…