Session Kit: Module 09: Neuron Morphology and Skeletonization
Everything needed to run Module 09 as a taught session: prep, timing, materials, misconceptions, rubric.
Generated from modules/module09.md. Edit the module page, not this file.
At a glance
| Duration | 4 hours |
| Capability target | Produce a skeleton-based morphology summary with at least three descriptors and one explicit limitation. |
| Learners leave with | Morphology descriptor table (10 neurons × 5 descriptors) |
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 01-08
Materials
Run of show
| Time | Segment | Your note |
|---|---|---|
| 00:00-10:00 | Morphology overview | |
| 10:00-24:00 | Skeleton extraction demo | |
| 24:00-38:00 | Descriptor calculation | |
| 38:00-50:00 | Interpretation and caveats | |
| 50:00-60:00 | Competency check |
The activity
Scenario: You have skeletons for 10 neurons in L2/3 of mouse visual cortex. Your task is to classify them as pyramidal vs interneuron based on morphology alone, then validate against synapse-based classification (excitatory vs inhibitory output synapses).
- Compute morphological descriptors for all 10 neurons (cable length, branch points, spine density, Strahler number, arbor volume).
- Create a summary table and scatter plot (e.g., spine density vs cable length).
- Classify each neuron as pyramidal or interneuron based on morphological criteria.
- Compare your morphological classification to the synapse-based classification (provided). Do they agree?
- For any mismatches, investigate: was the morphological measurement affected by reconstruction quality?
What learners hand in
- Morphology descriptor table (10 neurons × 5 descriptors)
- Scatter plot with proposed classification boundary
- Classification comparison table (morphology call vs synapse call)
- Brief report on any mismatches and their likely cause
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: A skeleton is a lossless summary of a neuron rather than a representation that discards surface geometry and spine shape.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
- They may believe: Morphological measurements are comparable across cells that were proofread to different levels.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
- They may believe: Total dendritic length is a property of the neuron rather than a property of the reconstruction of that neuron.
- Surface it by asking: “What would have to be true for that to hold? What would change your mind?”
- They may believe: A cell type assigned from morphology alone needs no corroboration from connectivity or molecular identity.
- 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: Valid skeleton and descriptor set for all neurons. At least 3 descriptors.
- Strong performance: Robust interpretation linking descriptors to cell-type identity. Explicit uncertainty framing for borderline cases. Investigation of mismatches.
- Common failure to flag: Descriptor list without biological context — reporting numbers without explaining what they mean for the neuron’s identity.
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
Explain one morphology feature that could be confounded by reconstruction quality.
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.