Session Kit: Module 04: Neuroanatomy for Connectomics
Everything needed to run Module 04 as a taught session: prep, timing, materials, misconceptions, rubric.
Generated from modules/module04.md. Edit the module page, not this file.
At a glance
| Duration | 4 hours |
| Capability target | Interpret a local EM region using correct anatomical context and document one confident and one uncertain structural call. |
| Learners leave with | Completed annotation table (patch ID, layer call, structure call, evidence, confidence) |
Before you walk in
- You can state the capability target in one sentence without reading it.
- You have one worked example you will narrate, including where you are unsure.
- Data access works — accounts, viewer, notebook — verified today, not last week.
- The rubric is visible to learners before they start, not after.
- You have decided what “uncertain” earns, and you will say so out loud.
Learners should arrive having covered:
- Modules 01-03
Materials
Run of show
| Time | Segment | Your note |
|---|---|---|
| 00:00-10:00 | Macro-to-micro bridge | |
| 10:00-24:00 | Guided structural identification | |
| 24:00-38:00 | Ambiguity case discussion | |
| 38:00-50:00 | Learner annotation round | |
| 50:00-60:00 | Debrief and competency check |
The activity
Scenario: You are given a set of 8 EM patches from a mouse cortex volume. The patches span different layers (L1 through L6) but are presented without layer labels.
- For each patch, determine the likely cortical layer using soma density, neuropil texture, and cell-type signatures.
- Identify the dominant cell type and compartment type in each patch.
- For each call, record the evidence chain and confidence level.
- Identify 2 patches where you are most uncertain and explain what additional information would help.
- Compare your annotations with a partner and resolve disagreements.
What learners hand in
- Completed annotation table (patch ID, layer call, structure call, evidence, confidence)
- Two uncertainty notes with proposed resolution strategies
- One “lesson learned” about how context changed an interpretation
Misconceptions to target
These are the errors this session exists to prevent. Surface them in the debrief rather than pre-empting them in the lecture — a misconception a learner has voiced is far easier to correct than one they are holding silently.
- They may believe: Cortical layer can be read off a single EM patch without soma density or neuropil context.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
- They may believe: The hippocampal laminar logic transfers to neocortex because both are cortex.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
- They may believe: An atlas coordinate is a ground-truth location rather than a registered estimate with a residual.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
- They may believe: Annotation confidence should be uniform across a volume, when boundaries and volume edges are systematically harder.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
Naming the norm
Every session is a chance to make one piece of the hidden curriculum explicit. Pick a moment where you would normally just do the professional thing, and say out loud why you are doing it — then ask whether anyone was taught that.
For this session, the candidate is whichever norm the activity most depends on: stating an assumption in the same sentence as the claim, recording the version a number came from, or saying “uncertain” and having it count as a real answer. See the hidden curriculum for the collected set and why naming them is a fairness intervention rather than etiquette.
Assessment
- Minimum pass: Context-aware call and confidence note for each patch. Layer identification is reasonable (within ±1 layer).
- Strong performance: Clear rationale linking EM features to layer context. Uncertainty is explicit and well-reasoned. Cross-slice evidence cited.
- Common failure to flag: Isolated local cue overconfidence — making a definitive call from a single feature without checking layer context or neighboring slices.
Grade the reasoning, not the answer. A correct call with no evidence chain should not outscore a well-reasoned incorrect one — and saying so publicly changes behaviour within one session.
Exit prompt
Describe one case where anatomy context changes your interpretation of an EM structure.
If this session goes wrong
- Nobody talks in the debrief. You asked “any questions?” Ask instead: “Which cue would you drop first if the data got worse?”
- Everyone finishes early. They are pattern-matching, not judging. Give an ambiguous case where the answer is “uncertain” and see what happens.
- Nobody finishes. The scaffolding came off too fast. Work the next case together rather than pressing on.
- A learner is silently lost. The most likely cause is unstated vocabulary. Point them at the dictionary and check back.