Module 03: Python and Jupyter for Neuroscience

Teaching Deck

Learning Objectives

  • Set up a reproducible notebook workflow
  • Load and inspect connectomics data tables
  • Write basic analysis and visualization code blocks
  • Document assumptions and outputs for reuse

Session Outcomes

  • Learners can complete the module capability target.
  • Learners can produce one evidence-backed artifact.
  • Learners can state one limitation or uncertainty.

Agenda (60 min)

  • 0-10 min: Frame and model
  • 10-35 min: Guided practice
  • 35-50 min: Debrief and misconception correction
  • 50-60 min: Competency check + exit ticket

Capability Target

Create a reproducible Jupyter notebook that ingests a connectomics dataset slice, performs one analysis, and exports documented outputs.

Concept Focus

Core Workflow

  • Set environment and dependencies.
  • Load dataset and validate schema.
  • Run analysis cell sequence.
  • Save outputs + metadata.
  • Re-run from clean kernel.

60-Minute Run-of-Show

  • 00:00-08: notebook anatomy.
  • 08:00-20: setup and loading.
  • 20:00-34: analysis coding sprint.
  • 34:00-46: plotting and export.
  • 46:00-56: clean rerun test.
  • 56:00-60: competency check.

Misconceptions to Watch

  • Surface and correct one likely misconception during debrief.

Studio Activity

Build a mini notebook with one descriptive statistic and one plot from a sample connectomics table.

Activity Output Checklist

  • Evidence-linked artifact submitted.
  • At least one limitation or uncertainty stated.
  • Revision point captured from feedback.

Assessment Rubric

  • Minimum: runnable notebook, clear outputs, basic metadata.
  • Strong: clean structure, robust error handling, repeatable rerun.
  • Failure: hidden state dependencies, undocumented assumptions.

Exit Ticket

Add one markdown cell documenting input version, processing steps, and output files.

References (Instructor)

  • Use module references listed on the module page.

Teaching Materials

  • Module page: /modules/module03/
  • Slide page: /modules/slides/module03/
  • Worksheet: /assets/worksheets/module03/module03-activity.md