Module 11 Activity Worksheet

Module: Module 11: Synapses and Circuit Logic
Duration: 4 hours
Generated from the module page. Edit modules/module11.md, not this file.

Capability target

Generate one synapse-to-motif interpretation with explicit evidence chain and one alternative explanation.

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 01-10

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 synaptic patterns support specific circuit hypotheses?
   • Your answer:
2. How do annotation errors alter motif conclusions?
   • Your answer:

The task

Scenario: You are analyzing a 200-neuron subgraph from the MICrONS dataset, spanning L2/3 and L4 of mouse visual cortex. Your goal: characterize the local circuit motif profile and identify any enriched patterns that suggest specific wiring rules.

1. Enumerate all 2-node and 3-node motifs in the subgraph (use DotMotif or equivalent tool).
2. Generate 1,000 degree-preserving random rewirings. Count motifs in each.
3. Compute z-scores for each motif type.
4. Identify the top 3 most enriched motifs. For each: draw the circuit diagram, propose a functional interpretation, and state one alternative explanation.
5. Write a 1-page “circuit logic brief” summarizing the motif profile of this circuit.

What you hand in

• Motif count table (observed vs expected vs z-score for each motif type)
• Circuit diagrams for top 3 enriched motifs
• 1-page circuit logic brief with interpretations and caveats

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.

• Identify synapse candidates: find synapses in the region of interest with correct pre/post assignment.
• Build local connectivity motif: extract the subgraph connecting the pre and post neurons and their immediate neighbors.
• Classify the motif: reciprocal pair, feed-forward loop, feedback inhibition, convergent input, etc.
• Evaluate against null: is this motif more common than expected?
• State supported claim (what the data shows) + caveat (what it doesn’t prove and what could confound it).

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: Asymmetric morphology means a synapse is excitatory, rather than putatively excitatory under a stated assumption.
• I did not assume: Reconstruction errors add symmetric noise to motif counts, when merges bias them toward denser motifs.
• I did not assume: A motif observed more often than expected is a functional building block.
• I did not assume: Synapse count is a direct measure of connection strength rather than a proxy for it.

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
  • The motif count table reports observed, expected, and z-score for every motif class examined, not only the enriched ones.
  • At least one motif carries a complete evidence chain: detection method, count, null comparison, and interpretation, in that order.
  • Each claim in the circuit logic brief is paired with an explicit caveat stating what it does not prove.
  • The synapse threshold and data version used to build the subgraph are stated in the brief.
• Strong performance
  • Every enriched motif has at least one non-functional alternative explanation (spatial proximity, cell-type composition, reconstruction error) named and, where possible, tested.
  • A second null model or a stratified analysis is applied to at least one motif, with the change in effect size reported.
  • Synapse-level evidence — compartment targeting, Gray type — is used to subdivide or qualify at least one motif class rather than treating graph edges as interchangeable.
  • Sensitivity to reconstruction quality is quantified: the headline count is re-run at a second synapse threshold or across proofreading versions, and the difference is reported.
• Common failure to flag
  • Motif claim without error-awareness — treating every enriched pattern as a functional circuit without considering artifacts or spatial confounds.
  • Functional language (“this circuit gates,” “this loop amplifies”) presented as a finding rather than as a consistency statement.
  • Enrichment reported against a single weak null with no statement of what it fails to control.

My self-assessment:

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

Exit prompt

Write one motif claim and one plausible confound.

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/module11/ · Slides: /modules/slides/module11/ · Facilitator guide