Research Assistant Position: Whole-Brain Imaging in Freely-Behaving Nematodes (fall 2025)

Research Assistant Position: Whole-Brain Imaging in Freely-Behaving Nematodes
Prof. Aravi Samuel and Helena Casademunt, Department of Physics/FAS
fall 2025

 

Freely-behaving animals constantly transform sensory inputs into internal representations, memories, and purposeful behavioral outputs. To do this, they use algorithms and circuits encoded in brain circuits. To make progress, we use accessible biophysical models of organism behavior that can be studied from sensory input to motor output. We primarily study navigational behaviors like chemotaxis and thermotaxis. In all of our studies, we apply expertise in optics and light microscopy. We build microscopes that allow us to manipulate and monitor the circuits that underlie behavior in freely-moving organisms. We use advanced high-throughput electron microscopy to map entire brain circuits at synaptic resolution. Responsibilities: We have recently developed a method to track the activity of every neuron in the brain of a freely-crawling nematode during chemotaxis and thermotaxis. We now seek the brain-wide representation of sensory processing and navigation. Requirements and Expectations: No previous experience, but some facility with computers is needed. The student will learn how to acquire whole-brain imaging datasets, and track and identify neurons throughout the worm brain. We use image analysis and machine-learning software to convert whole-brain image volumes into neural activity patterns. This is a very challenging problem for modern image analysis software, and so substantial human annotation and proofreading is needed to convert raw images into useful neural recordings. Additional Information: An unpaid 90r for the fall semester would be ideal. The necessary computers are in the lab in the Northwest Building, and so this is entirely "in person.” To Apply: Email Professor Samuel at samuel@physics.harvard.edu. (posted 9/25)