NeuroNauts

Project Sponsors

Mentor

Ogonna Eli
Faculty Mentor, Northern Arizona University

 Modern human society has disrupted sleep cycles for many. Disrupted sleep cycles from shift work, jet lag, or late nights can harm health and well being. Neurolight helps researchers study the brain’s circadian, master clock, advancing understanding of how neuronal rhythms impact daily life and health.
 Our project has two sponsors Dr. Charles Allen and Dr. Eck Doerry. Dr. Charles Allen, Ph. D, is a professor at Oregon Institute of Occupational Health science instructing a research lab that studies the correlation between environment factor and brian wave activities. Dr. Eck Doerry, Ph. D, is a professor at Northern Arizona University researching groupware systems. Our client wants to be able to use data collected more efficiently and effectively through a workbench. This workbench has to make some key features so researchers can provide effective outcomes to patients. So of the key features include:

• An analytic “workbench” to allow scientists to manage the entire analytic process, including a graphical interface (GUI) to manage the data input, choose specific types of analysis or adjust processing parameters, and quickly visualize and review resulting output.
  
• An analysis pipeline to determine the fluorescent intensity of individual neurons across a sequence of images taken every periodically over some time period (typically 30 minutes for seven days for this research, but the software workbench should support values/intervals).
  
• Output of quantitative fluorescence data for each neuron for further data analysis.
  
• A highly modular software architecture based around neuronal image processing “modules”. This project will create one such module (i.e., to support our specific analysis of circadian neuronal activity), but the software workbench should allow easy addition of novel modules in the future, to be able to support any sort of time lapse image series analysis of neuronal activity useful to other researchers.
  
• Must include a user manual for neuroscientist end-users, as well as strong architectural design and code documentation to support easy extension by future software teams.
  
• Software should be made available for easy end-user download and installation via Github, PyPi or similar sites (depending on choice of implementation languages) for use by the larger circadian rhythm research community.
  

 Our client has provided a starting point for their old workbench that was unorganized and messy. Our team plans to use some old parts of the software, algorithms, to build a new product for our client. We plan on making the new software less complicated for scientists to use, build a sense of certainty when scientists get results, and make the code updateable and manageable for years to come.

High-Level Requirements

• Import and manage time-series neuronal activity movies
• Provide workflow modules for circadian rhythm analysis
• Support statistical tests (Lomb-Scargle, Rao, Rayleigh)
• Export results in common formats for external analysis

These requirements were refined in collaboration with our sponsors as we iterated through the design process.