Introduction to Python and Jupyter notebooks for Neuroscience

NRSC 7610, Systems Neuroscience

University of Colorado School of Medicine, Anschutz Medical Campus

Daniel J Denman, 11 March 2024

This is an introduction to python for neuroscience, prepared for CU Anschutz NRSC7610 Systems Neuroscience and the CU Anschutz Neuroscience Graduate program

An instructor-led introductory notebook (Jupyter notebook, that is), NRSC7610_intro.ipynb, is the place to start. The class will all begin by running this notebook together, including the instructor, to get a feel for the basic syntax of Python and the flow of using a Jupyter notebook for data exploration and analysis. Students will complete the remainder of the Intro notebook in small groups or on their own, to develop confidence in independent coding.

optional extension and practice

After we go through the intro notebook together in class, you can choose one (or more!) of the exercise notebooks to work through. These notebooks will have a mixed of pre-written code and exercises, always towards an analysis goal typical for the modality. The four exercise notebook options are:

1. Direction Tuning Analysis
2. Time Series (Patch Clamp Vm) Analysis
3. Fluorenscene Image Analysis
4. RNASeq Analysis and Visualization
   
   Thanks to the Allen Institute for Brain Science and the Linnarson Lab for providing open data sets, and the Hughes Lab (Helena Barr specifically) for unpublished data!