Module 05: Electron Microscopy and Image Basics

Teaching Deck

Learning Objectives

  • Describe core EM acquisition concepts relevant to connectomics
  • Identify common image artifacts and likely downstream impact
  • Interpret image quality for segmentation readiness
  • Document uncertainty and QA decisions

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

Evaluate EM image patches for artifact risk and issue a justified pass/rework recommendation.

Concept Focus

  • Image quality as a scientific constraint.
  • Artifact taxonomy linked to downstream error.
  • QA gates and escalation logic.

Core Workflow

  • Inspect image quality and artifact signatures.
  • Classify severity and likely impact.
  • Decide pass/rework with rationale.
  • Log findings for reproducibility.

60-Minute Run-of-Show

  • 00:00-08: EM basics refresher.
  • 08:00-20: artifact recognition walkthrough.
  • 20:00-34: learner triage round.
  • 34:00-46: QA threshold debate.
  • 46:00-56: decision logging practice.
  • 56:00-60: competency check.

Misconceptions to Watch

  • Surface and correct one likely misconception during debrief.

Studio Activity

Classify 6 patches by artifact type/severity and propose action.

Activity Output Checklist

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

Assessment Rubric

  • Minimum: accurate major artifact calls + action decision.
  • Strong: clear impact reasoning and consistent thresholds.
  • Failure: artifact labels without downstream implications.

Exit Ticket

Pick one artifact and explain how it could create a merge or split error later.

References (Instructor)

  • Use module references listed on the module page.

Teaching Materials

  • Module page: /modules/module05/
  • Slide page: /modules/slides/module05/
  • Worksheet: /assets/worksheets/module05/module05-activity.md