Understanding when, how, and if bacteria swim is key to understanding critical ecological and bio... more Understanding when, how, and if bacteria swim is key to understanding critical ecological and biological processes, from carbon cycling to infection. Imaging motility by traditional light microscopy is limited by focus depth, requiring cells to be constrained in z. Holographic microscopy offers an instantaneous 3D snapshot of a large sample volume, and is therefore ideal in principle for quantifying unconstrained bacterial motility. However, resolving and tracking individual cells is difficult due to the low amplitude and phase contrast of the cells; the index of refraction of typical bacteria differs from that of water only at the second decimal place. In this work we present a combination of optical and samplehandling approaches to facilitating bacterial tracking by holographic phase imaging. The first is the design of the microscope, which is an off-axis design with the optics along a common path, which minimizes alignment issues while providing all of the advantages of off-axis holography. Second, we use anti-reflective coated etalon glass in the design of sample chambers, which reduce internal reflections. Improvement seen with the antireflective coating is seen primarily in phase imaging, and its quantification is presented here. Finally, dyes may be used to increase phase contrast according to the Kramers-Kronig relations. Results using three test strains are presented, illustrating the different types of bacterial motility characterized by an enteric organism (Escherichia coli), an environmental organism (Bacillus subtilis), and a marine organism (Vibrio alginolyticus). Data processing steps to increase the quality of the phase images and facilitate tracking are also discussed.
Proceedings of the Twenty-Second National Radio Science Conference, 2005. NRSC 2005., 2005
In the present paper, under thermal operating conditions, the performance characteristics of high... more In the present paper, under thermal operating conditions, the performance characteristics of high speed laser diode (based on vertical cavity surface emitting laser (VCSEL)) is deeply and parametrically investigated. The processed characteristics are : the harmonic response transfer function, both the resonance frequency and 3-dB band-width, and the rise time. These diodes affect the transmitted bit-rate in high-speed advanced optical communication systems. The effects of both ambient temperature (and consequently the inner temperature) and the injected current (power) are deeply investigated. The pulse rise time, and the resonance frequency as well as the 3-dB bandwidth are the major criterions of the device speed. It is found that the device undergoes good performance: higher resonance frequency, higher bandwidth, and smaller rise time as the proposed figure of merit increases
Digital Holographic Microscopy (DHM) is an emerging technique for three-dimensional imaging of mi... more 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 success for use with eukaryotes, it has proven challenging for bacterial imaging because of low contrast and sources of noise intrinsic to the method (e.g. laser speckle). This paper describes a custom written MATLAB routine using machinelearning algorithms to obtain three-dimensional trajectories of live, lab-grown bacteria as they move within an essentially unrestrained environment with more than 90% precision. A fully annotated version of the software used in this work is available for public use.
Understanding when, how, and if bacteria swim is key to understanding critical ecological and bio... more Understanding when, how, and if bacteria swim is key to understanding critical ecological and biological processes, from carbon cycling to infection. Imaging motility by traditional light microscopy is limited by focus depth, requiring cells to be constrained in z. Holographic microscopy offers an instantaneous 3D snapshot of a large sample volume, and is therefore ideal in principle for quantifying unconstrained bacterial motility. However, resolving and tracking individual cells is difficult due to the low amplitude and phase contrast of the cells; the index of refraction of typical bacteria differs from that of water only at the second decimal place. In this work we present a combination of optical and samplehandling approaches to facilitating bacterial tracking by holographic phase imaging. The first is the design of the microscope, which is an off-axis design with the optics along a common path, which minimizes alignment issues while providing all of the advantages of off-axis holography. Second, we use anti-reflective coated etalon glass in the design of sample chambers, which reduce internal reflections. Improvement seen with the antireflective coating is seen primarily in phase imaging, and its quantification is presented here. Finally, dyes may be used to increase phase contrast according to the Kramers-Kronig relations. Results using three test strains are presented, illustrating the different types of bacterial motility characterized by an enteric organism (Escherichia coli), an environmental organism (Bacillus subtilis), and a marine organism (Vibrio alginolyticus). Data processing steps to increase the quality of the phase images and facilitate tracking are also discussed.
Proceedings of the Twenty-Second National Radio Science Conference, 2005. NRSC 2005., 2005
In the present paper, under thermal operating conditions, the performance characteristics of high... more In the present paper, under thermal operating conditions, the performance characteristics of high speed laser diode (based on vertical cavity surface emitting laser (VCSEL)) is deeply and parametrically investigated. The processed characteristics are : the harmonic response transfer function, both the resonance frequency and 3-dB band-width, and the rise time. These diodes affect the transmitted bit-rate in high-speed advanced optical communication systems. The effects of both ambient temperature (and consequently the inner temperature) and the injected current (power) are deeply investigated. The pulse rise time, and the resonance frequency as well as the 3-dB bandwidth are the major criterions of the device speed. It is found that the device undergoes good performance: higher resonance frequency, higher bandwidth, and smaller rise time as the proposed figure of merit increases
Digital Holographic Microscopy (DHM) is an emerging technique for three-dimensional imaging of mi... more 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 success for use with eukaryotes, it has proven challenging for bacterial imaging because of low contrast and sources of noise intrinsic to the method (e.g. laser speckle). This paper describes a custom written MATLAB routine using machinelearning algorithms to obtain three-dimensional trajectories of live, lab-grown bacteria as they move within an essentially unrestrained environment with more than 90% precision. A fully annotated version of the software used in this work is available for public use.
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Papers by Marwan Elkholy