Monitoring the Rizosphere with Optics

Light is a key factor for the growth of plant life. Most are familiar with the need for plants to be exposed to light for photosynthesis, but recent findings have found that light is not only important for the parts of the plant that are above ground, but that the underground root structure also senses the above ground conditions by channeling light through the stem of the plant. The goal of this project will be to start a new investigation of the commonly-used Arabidopsis plant model by growing plants from seedlings and analyzing the root structures and their ability to conduct light.

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.

Logistics Information:
Project categories
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
Fall - Part Time
Spring - Part Time
Summer - Full Time
Academic Credit
Paid Research
Number of openings
Techniques learned
  • Fundamental microscopy concepts
  • Fourier Optics
  • Computational microscopy
  • Computational imaging algorithms
Contact Information:
Josh Brake
Principal Investigator
Name of project director or principal investigator
Prof. Josh Brake
Email address of project director or principal investigator
2 sp. | 7 appl.
Hours per week
Fall - Part Time (+2)
Fall - Part TimeSpring - Part TimeSummer - Full Time
Project categories