Light Propagation in a Temporal Focusing Microscope using Matlab
Submission information
Submission Number: 10
Submission ID: 27
Submission UUID: 9d38cbfb-bb83-457a-86a2-0a90a9cccce6
Submission URI: /form/project
Created: Fri, 08/30/2019 - 11:49
Completed: Fri, 08/30/2019 - 11:53
Changed: Thu, 05/05/2022 - 04:44
Remote IP address: 130.215.55.243
Submitted by: Northeast Cyberteam
Language: English
Is draft: No
Webform: Project
Light Propagation in a Temporal Focusing Microscope using Matlab
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Project Leader
Project Personnel
Project Information
Understanding the propagation of light is essential for developing new techniques for biomedical optics. Characterizing the resolution of a microscope requires calculating how light travels through optical elements such as lenses, apertures, and diffraction gratings. This project uses Fourier optics to analyze the propagation of light through a temporal focusing microscope, in which laser pulses pass through a diffraction grating, a collimating lens, and an objective lens on their way to the sample. Because each wavelength can be treated independently, a cluster will perform parallel numerical calculations to reconstruct the light field at the focus of the microscope, allowing for a more complete understanding of how different laser parameters affect the resolution of a temporal focusing microscope.
Project Information Subsection
The major goal of this project is to develop a protocol for running Matlab code on the institution’s new server. The PI has no experience with using a cluster, but this particular Matlab code cannot run in a reasonable amount of time on a college-issued computer. Once the current version of the code is up and running, the student will need to further optimize the simulation for running on the cluster. With any time remaining, the student will apply different phase profiles to the beam to characterize how it affects the quality of the focus, which is novel and should lead to a publication
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The PI has written the wave propagation code in Matlab, and this project needs a student who can transform the calculations to run on a cluster. Because Matlab will also be installed on the cluster, the student will be responsible for developing the workflow for running the simulation on the cluster, as well as to enhance the existing code to take advantage of the cluster’s parallel computing power. The ideal candidate would be an undergraduate student at the PI’s home institution.
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Middlebury College
276 Bicentennial Way
McCardell Bicentennial Hall
Middlebury, Vermont. 05753
McCardell Bicentennial Hall
Middlebury, Vermont. 05753
NE-University of Vermont
09/09/2019
No
Already behind3Start date is flexible
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It would be great to add a tutorial for others to run traditional Matlab code on a cluster, particularly for novices like myself who have never used a cluster before.
Once the code matches the known results for a normal Gaussian beam passing through the microscope optics, the student and the PI can then start adding different spectral phase shifts to the pulse. Because a diffraction grating spreads the different wavelengths out in space, a spectral phase shift becomes a spatial phase shift, causing a change in the way the beam focuses. Higher-order-polynomial phase shifts in a temporal focusing microscope have not been explored, and such a calculation combined with new experimental data will provide the basis of our next paper.
In addition to high performance computing, the student will learn about geometric optics, wave optics, and Fourier optics. The student will make connections between the Fourier transform of a continuous function and the discrete Fourier transform when using simulated discrete data. Lastly, the student will discover how their physics and optics knowledge translate to the field of biomedical optics.
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The Cyberteam program supports researchers in need of high performance computing resources, and this project requires help in using a cluster that is new to the PI, the student, and their institution. While the Cyberteam already has much experience, the program will enhance its skills in communicating HPC approaches to complete novices.
This project will use Matlab on the new cluster at Middlebury College. Typically, the electric fields of 16384 wavelengths are simulated in 2D space with 65536 x 65536 arrays. Each of these need to be propagated to approximately 256 different axial positions. For double precision, this comes out to 65536 x 65536 x 8 bytes = 34 GB per array, run in parallel 16384 times, run in a loop 256 times. While the parameters will likely change, it takes too long to run on a regular desktop computer to even begin to explore ways of optimizing the size of the arrays.
Prof. Chris Herdman (Middlebury College) told me about this opportunity after hearing about it from Prof. Adrian Del Maestro (UVM). I am interested in supporting one Middlebury College student through this program in Fall 2019 and possibly beyond.
Final Report
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