Benthic Underwater Microscope

Microscope_LabImage4 - Pocillopora - 4.2x3.5_FOV - FluorescenceSponsors: W. M. Keck Foundation, National Science Foundation

Project Overview: 
Micro-scale activities drive many important changes in marine ecosystems and ideally such processes should be observed in the natural environment. The Benthic Underwater Microscope (BUM) is a diver operated instrument designed in the Jaffe Lab to take microscopic images and video of seafloor environments such as coral reefs.

General Information:

The BUM is the first instrument capable of collecting non-invasive, underwater recordings of these benthic environments at nearly micrometer resolution. To achieve its capabilities the instrument’s design includes focused LED’s for illumination, a long working microscope objective lens for magnification, and an electrically tunable lens for focusing. Additionally an underwater computer allows active user control by a scientific diver.

Using the BUM we have collected in-situ time-series recordings of coral polyps including feeding behaviors and inter-polyp competition. Additionally we have studied coral bleaching and subsequent overgrowth by algae. Details about this work, including underwater images and video, can be found in the article “Underwater microscopy for in situ studies of benthic organisms” published in the journal Nature Communications:


  • Principal Investigators: Jules S. Jaffe
  • Principal Engineers: Andrew Mullen, Tali Treibitz
  • Engineering Consultant: Paul L. D. Roberts
  • Graduate Students: Andrew Mullen


This article received wide media coverage by outlets including: New York Times, Los Angeles Times, Washington Post, BBC, National Geographic, MIT Technology Review, and more. Links to these articles be found here.