The brain is the most complex organ of the body, and hosts a multitude of cell types organized in functionally-specialized brain regions. So far, systematic attempts to describe the complexity of the brain have been limited to a few species, including mouse and the fruit fly. Extending the description of brains to multiple species is essential to identify evolutionarily-conserved principles of brain organization and function.

The Tosches lab has developed a new exciting tool to visualize the expression of any gene in the entire brain of salamanders. Specifically, we have collected volumetric imaging data for selected marker genes, using brain clearing combined with new methods for in situ hybridization.

The goal of this DSI Scholars project is to integrate these volumetric imaging data into a reference atlas of the salamander brain. This involves (1) the generation of an average brain volume (2) the alignment of individual imaging volumes to the average brain (3) the data-driven segmentation of the average brain into brain regions.

Experience with python is required.

This project is eligible for a matching fund stipend from the Data Science Institute. This is not a guarantee of payment, and the total amount is subject to available funding.

Faculty Advisor

Project Timeline

  • Earliest starting date: 4/1/2022
  • End date:
  • Number of hours per week of research expected during Spring/Summer 2022: ~10
  • Number of hours per week of research expected during Summer 2022: ~40

Candidate requirements

  • Skill sets: fluency in python
  • Student eligibility: freshman, sophomore, junior, senior, master’s
  • International students on F1 or J1 visa: eligible
  • Academic Credit Possible: No