Module 05 Activity Worksheet

Module: Module 05: Electron Microscopy and Image Basics
Duration: 4 hours
Generated from the module page. Edit modules/module05.md, not this file.

Capability target

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

You are done when you can demonstrate this, not when you have filled in every box below.

Before you start

Check that you have:

• Modules 01-04

Bring one question you already have about this topic. Write it here so you can check at the end whether it was answered:

My question:

Questions this module answers

Keep these in view. At the end, answer each in one sentence.

1. Which artifacts critically affect reconstruction quality?
   • Your answer:
2. What minimum image quality supports downstream segmentation?
   • Your answer:

The task

Scenario: Your team has received pilot images from a new ssTEM acquisition of mouse visual cortex. The imaging facility reports that initial sections looked good, but they encountered intermittent knife chatter starting around section 200 and a possible staining gradient in the lateral third of the field of view. Before the facility commits to imaging the remaining 800 sections, your team must evaluate the pilot data and deliver a go/no-go recommendation with conditions.

1. Survey (10 min): Open the six provided image patches (three from the clean region, three from the reported problem areas). For each patch, independently record: modality confirmation, visible artifacts, and an initial severity impression.
2. Artifact classification (15 min): Using the artifact reference card, formally classify each artifact by type and assign a severity score (1 = minor, cosmetic; 2 = moderate, segmentation-affecting; 3 = severe, reconstruction-blocking). Map each artifact to its expected segmentation consequence (merge, split, or topology break).
3. Spatial pattern analysis (10 min): Arrange the patches by their spatial position in the volume. Determine whether the artifacts are spatially correlated (e.g., staining gradient affecting one side consistently) or random. Spatially correlated artifacts require different mitigation than random ones.
4. Cost-benefit analysis (10 min): For each artifact, estimate the downstream cost if the facility proceeds without fixing it. Consider: how many proofreading hours per affected section? How many sections are likely affected? Compare this to the cost of pausing acquisition for knife replacement or re-staining.
5. Recommendation memo (15 min): Write a one-page memo to the imaging facility with your team’s recommendation. The memo must include: (a) a summary table of artifacts found, (b) your go/no-go decision with conditions, (c) specific remediation steps if you recommend pausing, and (d) a monitoring plan if you recommend proceeding.

What you hand in

• Completed QA worksheet for all six patches
• Spatial artifact map (annotated sketch or diagram)
• One-page recommendation memo with summary table

Working checklist

Tick as you go. If you skip a step, write why — a skipped step with a stated reason is a decision; a skipped step without one is a gap.

• Inspect image quality and artifact signatures.
• Classify severity and likely impact on segmentation.
• Decide pass/flag/rework with documented rationale.
• Log findings in a structured QA record for reproducibility.

Evidence and reasoning

Fill one row per claim you make in your artifact. A claim without a limitation is not finished.

Confidence. For your main claim, mark one and say why:

• High — two or more independent lines of evidence agree
• Medium — one strong line, or several that share a weakness
• Uncertain — the deciding evidence is not available to me

Why:

One alternative I considered and rejected, and the reason:

Misconception self-check

These are the errors this module is designed to prevent. Confirm you did not make them, or note where you nearly did:

• I did not assume: You can proofread your way out of a bad image.
• I did not assume: A noisy image is worse for segmentation than a clean image with faint membranes.
• I did not assume: Artifact severity can be judged from a count, when the spatial distribution matters more.
• I did not assume: Quality assessment is a clerical checkpoint rather than a scientific judgment that propagates through every downstream claim.

Session timing (facilitator reference)

Rubric

Score yourself before anyone else does. Where you fall short, name the specific next action rather than a general intention.

• Minimum (pass): Accurate identification of major artifacts across all patches, correct mapping to segmentation error type, and a defensible pass/flag/rework decision for each patch.
• Strong (merit): Clear articulation of cost tradeoffs, consistent severity thresholds across patches, spatially aware analysis, and a well-structured recommendation memo with specific conditions.
• Failure: Artifact labels assigned without reference to downstream segmentation implications, or QA decisions made without documented rationale.

My self-assessment:

• Strongest part of my work, and the evidence for that:
• Weakest part, and the specific next action:

Exit prompt

Pick one artifact and explain how it could create a merge or split error later. Then estimate: if this artifact appears on 5% of sections, how many additional proofreading hours would it add to a 1000-section volume?

Your answer:

Peer review (swap worksheets)

Reviewing someone else’s reasoning is the fastest way to see the gaps in your own. Assess the evidence quality, not whether you agree with the conclusion.

• Is every claim paired with specific evidence?
• Is at least one limitation stated, and is it a real one?
• Is the confidence level justified by the number of independent evidence lines?
• One thing this person did better than me:
• One question I would ask them:

Module page: /modules/module05/ · Slides: /modules/slides/module05/ · Facilitator guide