03 EM Prep and Imaging

Technical Training: Nanoscale Connectomics

Learning goals

• Understand prep-to-imaging chain.
• Identify artifact classes and downstream impact.

Acquisition chain

Fixation -> Staining -> Sectioning/Block-face -> Imaging -> Stack assembly

Artifact classes

• Physical: tears, folds, chatter, compression.
• Signal: charging, contrast drift.
• Geometric: misalignment and seam artifacts.

Why artifacts matter

Acquisition defects propagate to segmentation merges/splits and topology errors.

QA gates

• SNR and intensity drift checks.
• Seam residual monitoring.
• Missing/damaged section tracking.

Pilot-first strategy

Run pilot segmentation before full-volume ingestion.

Failure modes

• Late QA discovery.
• Missing acquisition metadata.
• Throughput-over-fidelity decisions without quantified cost.

Activity

Create a risk register with 3 artifacts, metrics, and mitigation triggers.

Bridge

Next unit: infrastructure that operationalizes this data at scale.