Dataset Information

Six-pack holography for dynamic profiling of thick and extended objects by simultaneous three-wavelength phase unwrapping with doubled field of view.

ABSTRACT: Dynamic holographic profiling of thick samples is limited due to the reduced field of view (FOV) of off-axis holography. We present an improved six-pack holography system for the simultaneous acquisition of six complex wavefronts in a single camera exposure from two fields of view (FOVs) and three wavelengths, for quantitative phase unwrapping of thick and extended transparent objects. By dynamically generating three synthetic wavelength quantitative phase maps for each of the two FOVs, with the longest wavelength being 6207 nm, hierarchical phase unwrapping can be used to reduce noise while maintaining the improvements in the 2π phase ambiguity due to the longer synthetic wavelength. The system was tested on a 7 μm tall PDMS microchannel and is shown to produce quantitative phase maps with 96% accuracy, while the hierarchical unwrapping reduces noise by 93%. A monolayer of live onion epidermal tissue was also successfully scanned, demonstrating the potential of the system to dynamically decrease scanning time of optically thick and extended samples.

SUBMITTER: Mirsky SK

PROVIDER: S-EPMC10630357 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Publications

Six-pack holography for dynamic profiling of thick and extended objects by simultaneous three-wavelength phase unwrapping with doubled field of view.

Mirsky Simcha K SK Shaked Natan T NT

Scientific reports 20231107 1

Dynamic holographic profiling of thick samples is limited due to the reduced field of view (FOV) of off-axis holography. We present an improved six-pack holography system for the simultaneous acquisition of six complex wavefronts in a single camera exposure from two fields of view (FOVs) and three wavelengths, for quantitative phase unwrapping of thick and extended transparent objects. By dynamically generating three synthetic wavelength quantitative phase maps for each of the two FOVs, with the ...[more]

PMID: 37935758

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Project description:We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including non-homogeneous transition rates along mRNA, the fact that every ribosome covers several codons, and the fact that ribosomes cannot overtake one another. The RFMEO is a mean-field approximation of an important model from statistical mechanics called the totally asymmetric simple exclusion process with extended objects (TASEPEO). We demonstrate that the RFMEO describes biophysical aspects of translation better than previous mean-field approximations, and that its predictions correlate well with those of TASEPEO. However, unlike TASEPEO, the RFMEO is amenable to rigorous analysis using tools from systems and control theory. We show that the ribosome density profile along the mRNA in the RFMEO converges to a unique steady-state density that depends on the length of the mRNA, the transition rates along it, and the number of codons covered by every ribosome, but not on the initial density of ribosomes along the mRNA. In particular, the protein production rate also converges to a unique steady state. Furthermore, if the transition rates along the mRNA are periodic with a common period T then the ribosome density along the mRNA and the protein production rate converge to a unique periodic pattern with period T, that is, the model entrains to periodic excitations in the transition rates. Analysis and simulations of the RFMEO demonstrate several counterintuitive results. For example, increasing the ribosome footprint may sometimes lead to an increase in the production rate. Also, for large values of the footprint the steady-state density along the mRNA may be quite complex (e.g. with quasi-periodic patterns) even for relatively simple (and non-periodic) transition rates along the mRNA. This implies that inferring the transition rates from the ribosome density may be non-trivial. We believe that the RFMEO could be useful for modelling, understanding and re-engineering translation as well as other important biological processes.

Dataset Information

Six-pack holography for dynamic profiling of thick and extended objects by simultaneous three-wavelength phase unwrapping with doubled field of view.

Publications

Six-pack holography for dynamic profiling of thick and extended objects by simultaneous three-wavelength phase unwrapping with doubled field of view.

Similar Datasets

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