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