Module 03: Navigating the Scientific Method in Connectomics

Learn how the scientific method guides brain mapping, and develop your ability to ask testable neuroscience questions.

Overview

This module explores the scientific method as applied to connectomics and computational neuroscience. Learners will break down the steps of hypothesis generation, experimental design, data collection, analysis, and interpretation within the context of brain circuit mapping. It also introduces real-world case studies from published connectomics research.

SMART Learning Objectives

By the end of this module, students will be able to:

  • Explain the steps of the scientific method in the context of neuroscience research. (Bloom: Understand)
  • Differentiate between observational studies and hypothesis-driven experiments. (Bloom: Analyze)
  • Formulate a basic hypothesis related to brain connectivity or structure. (Bloom: Apply, Create)

Training Goals

  • Connect foundational research methodology with neuroscience-specific challenges.
  • Introduce experimental paradigms in connectomics (e.g., tracing, volume imaging).
  • Empower students to ask tractable, testable scientific questions.

Core Scientific Method Stages (Connectomics Examples)

  • Ask a Question (e.g., How are inhibitory neurons organized?)
  • Formulate a Hypothesis (e.g., Inhibitory axons preferentially target dendritic shafts)
  • Design an Experiment (EM volume + cell type labels + tracing)
  • Collect Data (Segmentations, synapse detection, tracing)
  • Analyze & Interpret (Statistical testing, visualization)

Key Resources

Sample Colab Notebook

Coming soon – Interactive notebook guiding learners to generate testable hypotheses based on EM datasets.

Public Videos / Open Courses

Assessment

  • Worksheet: Match each step of the scientific method to a real-world connectomics example.
  • Discussion Prompt: Propose a tractable question that could be answered using electron microscopy (EM) data.

COMPASS Integration

This module integrates key COMPASS skills:

  • Research Fundamentals: How to ground investigations in the scientific method.
  • Scientific Reasoning: Translating big questions into testable hypotheses.

While designed around connectomics, these skills generalize to all STEM research domains. Alternative examples from physics, chemistry, or computational biology may be substituted as needed in class discussions.

Framework Alignment

MERIT Stage: Orientation & Research Foundations
CCR Pillars: Knowledge, Meta-Learning
Scientific Pipeline: Scientific Question