Shampoo for SHAMU

Astronomy and Astrobiology grad student Brett Morris’ research rotation let him swap his telescope for a microscope as he learned about techniques for detecting life on the Solar System’s icy worlds.

By Brett Morris

Graduate Student, Astronomy & Astrobiology


The planetary science and astrobiology communities have elevated Saturn’s icy moon Enceladus to the ranks of Titan and Europa as a top-priority icy world worthy of study for astrobiology. Enceladus exhibits cryovolcanism, with material from the planet’s interior being ejected into space, which presents an opportunity for a future orbiter or lander to directly sample ice that originated in Enceladus’ warm interior. Cassini mass spectrometry of Enceladus’ plumes also reveals organic matter, begging the question: since worlds like Enceladus may have conditions that could support life, how do we best search for signs of life on icy worlds in the solar system? 

In my research rotation project, I was privileged to join a team of interdisciplinary experts on microbial motility and holographic microscopy who seek to test the hypothesis: “is microbial motility an unambiguous biosignature of extant life?” We know that organisms on Earth have innumerable reasons to move; for example, organisms move towards nutrients, away from toxins, towards heat, towards light. Perhaps life on worlds like Enceladus would evolve motility as well. One advantage of searching for microbial motility, rather than searching for ATP or DNA, is that the motility hypothesis is agnostic about the chemistry of the organisms that are moving, so long as the organisms move. 

We are testing this hypothesis by studying motile terrestrial microbes with SHAMU – or the “Submersible Holographic Astrobiology Microscope with Ultraresolution” led by PI Jay Nadeau, (Portland State University). SHAMU is a digital holographic microscope (DHM) with ~1 micron resolution. The hardware required is compact, requires comparatively little energy and no moving parts, which makes it a good candidate for future space exploration missions. 

Digital holographic microscopes use interferometry to measure perturbations imparted on the phase and amplitude of a laser beam by small specimens – on scales similar to the wavelength of the laser (300 nm). The holograms recorded by the DHM encode the full phase and amplitude of the light at every position in the fluid sample chamber, allowing us to locate the 3D positions of specimens in each hologram. Time-series holography allows us to measure the full 3D velocities of the specimens as they move with bulk flow in the fluid, and as they swim.  Unambiguously detecting this difference between bulk flow and swimming – algorithmically, and with minimal human intervention – is the near-term goal of the SHAMU project. 

One of the primary obstacles to achieving this goal is a computational bottleneck. Each hologram recorded by the microscope must be processed to recover the phase and amplitude information – this process is called hologram reconstruction. When I began working with the SHAMU team, all reconstructions were completed with proprietary, “black-box” software (Koala Acquisition & Analysis by Lyncée Tec), for which the group had a limited number of licenses. It could take several days for the software to finish reconstructions for an hour’s worth of microscope observations. 

My contribution to the SHAMU project was to create the first open source numerical holographic reconstruction toolkit in Python, which could be used alongside or in place of the proprietary software. There are several advantages to creating our own software pipeline: (1) we know what the software is doing at each step in the reconstruction process, (2) we can tweak the reconstruction algorithm to suit our motility observations, (3) the free software is platform independent and can be used on as many machines as you have access to (no license necessary), (4) despite being written in Python, which is generally thought of as a “slow” language, our pipeline is more efficient than the alternative package with limited licenses, because you can run our free software with many reconstruction jobs in parallel, greatly reducing the wall clock time for a given reconstruction.

Many of the tasks necessary for numerical reconstruction of digital holograms are performed manually by microscope users. For example, the user might be required to create a real-image mask in Fourier-space, and to select background regions of a reconstructed image, which are used to train aberration correction routines. These steps are redundant if the holographic microscope configuration that doesn’t change significantly from one observation to the next, and if the area of the image occupied by specimens is typically small compared to the background –as is the case when working with unresolved specimens. The software I developed takes advantage of these opportunities to automate the reconstruction and aberration correction processes.

The software package, dubbed “shampoo”, has been adopted by the SHAMU group, and I continue to lead code development and maintenance in collaboration with J. Kent Wallace and Santos Fregoso (NASA JPL). We are in the early stages of writing up a paper for submission to the journal Applied Optics on the many design decisions that went into our custom-tailored reconstruction algorithm. The source code is freely available on GitHub*

In this project I learned so much that it’s hard to summarize concisely, thanks to the guidance of my advisor Professor Jody Deming, her graduate student Max Showalter, and the rest of the SHAMU team. I learned about the types of microbial motility, I learned how digital holographic microscopy works, I wrote a numerical reconstruction algorithm from scratch, I learned how to collaborate in a large research group with experts across many non-overlapping disciplines, and perhaps most importantly, I learned how to better communicate my work with the others in the group. It has been one of the greatest privileges of my graduate career to work with this group, and I thank the UW Astrobiology Program for its support in making my research rotation appointment possible.

* Source code: