3d-printed Computational Microscopy using Fourier Ptychography

Project Description

The goal of this project is to develop a computational microscope using the UC2 system, a 3-D printed, reconfigurable optics platform that can be used to build compact and flexible optical systems. In particular, we will be implementing a microscopy technique called Fourier Ptychographic Microscopy (FPM) using the UC2 platform. You will have the opportunity to explore both experimental and computational aspects by building and working with a physical UC2 system and by collecting and processing your own experimental data.

Traditional optical systems trade off resolution and field of view. For example, consider a typical camera. You can either zoom out and capture a wide scene without fine details or you can zoom into the scene (e.g., by choosing a higher magnification lens) which enables you to resolve finer details, but at the price of a smaller field of view. This tradeoff is the result of the physical limits on the amount of information that can pass through an optical system.

However, recent advances in computation and digital cameras have provided opportunities to creatively bypass this limit. In particular, by rethinking the illumination scheme used in traditional imaging models, we can mix additional information into our images which can then be exploited in an image reconstruction algorithm to recover more information about our sample. In FPM, this is achieved by replacing the standard light source used in a microscope with a light emitting diode (LED) array. Then, by turning on different combinations of LEDs, we can introduce additional information into the captured images. This additional information enables high-resolution imaging with a wide field of view. In addition, the reconstruction algorithm further enables desirable features such as the ability to digitally refocus captured images, improve the contrast of transparent samples like cells which typically are hard to see in conventional microscopes, and correct for imperfections in the lenses of the microscope.

Relevant Papers

Note: Research in the Spring will take place regardless of whether research can be conducted on campus at Mudd but Summer research positions may be contingent on whether in-person research on campus is possible.

Application Materials: Please include a resume, unofficial transcript, and a short essay explaining why you are interested in working on this research project, what skills and experiences you bring to the project, and what do you hope to learn from this experience.

Name of research group, project, or lab
HMC Biophotonics Lab
Why join this research group or lab?

As a member of the HMC Biophotonics Lab you will join a passionate group of budding researchers exploring the field of biophotonics and connecting your existing knowledge to generate new ideas. This project will help to create low-cost, compact, and reconfigurable optical microscopes which can be used for a variety of applications including laboratory imaging for diagnostics and for education.

In addition to this project, there are other efforts in the lab to develop optical tools to focus light deep into tissue by counteracting the scattering effect of biological tissue.

Logistics Information:
Project categories
Biomedical Sciences
Signal Processing
Student ranks applicable
Student qualifications

This research is accessible to all academic levels and requires only some introductory physics and computer programming to start. The following skills are helpful but not required:

  • CS Coursework: CS5, CS60, CS70, CS144/MATH164
  • Engineering Coursework: E79; E85
  • Physics Coursework: Ph51, Ph57c, Ph134, Ph151
  • Programming Experience: Python, Matlab, C

The most important qualifications are a curious and can-do attitude and the willingness to try, fail, and try again.

Time commitment
Spring - Part Time
Summer - Full Time
Academic Credit
Number of openings
Techniques learned
  • Fundamental microscopy concepts
  • Fourier Optics
  • Computational microscopy
  • Computational imaging algorithms
Contact Information:
Mentor name
Josh Brake
Mentor email
Mentor position
Principal Investigator
Name of project director or principal investigator
Prof. Josh Brake
Email address of project director or principal investigator
2 sp. | 13 appl.
Hours per week
Spring - Part Time (+1)
Spring - Part TimeSummer - Full Time
Project categories
Biomedical Sciences (+2)
Biomedical SciencesOpticsSignal Processing