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H01 electron microscopy with object segmentation and original 2 µm scale bar Nanoscale · Module 01

Scientific Curiosity and Motivation

Teaching Deck

Human cortex · H01
Object segmentation over electron microscopy

H01 release · Lichtman Lab / Harvard & Connectomics at Google · CC BY 4.0
Shapson-Coe et al. (2024) · doi:10.1126/science.adk4858

Module 01 · Nanoscale

Learning Objectives

  • Explain why connectomics matters scientifically
  • Formulate one testable connectomics question
  • Distinguish motivating narratives from evidence-backed claims
  • Identify personal learning goals for the technical track
Module 01 · Nanoscale

Capability Target

Write one connectomics study question with measurable structural outputs and one explicit non-claim. Articulate a personal motivation statement linking daily annotation work to a larger scientific mission.

Module 01 · Nanoscale

Concept Focus

1) Question before method

  • Technical: define target measurement before tool choice.
  • Plain language: know what you are asking first.
  • Misconception guardrail: tools generate good questions automatically.
Module 01 · Nanoscale

Core Workflow

  • Identify curiosity question.
  • Convert to measurable structural hypothesis.
  • Define one metric and one limitation.
  • Plan first dataset/tool touchpoint.
Module 01 · Nanoscale

Core Workflow (continued)

  • Write a personal motivation statement connecting your question to a long-term scientific goal.
Module 01 · Nanoscale

Run of Show (90 min)

  • Block 1: Opening hook (00:00-12:00)
  • Block 2: Connectomics landscape (12:00-28:00)
  • Block 3: Question framing workshop (28:00-48:00)
  • Block 4: Evidence-boundary critique (48:00-65:00)
Module 01 · Nanoscale

Run of Show (90 min) (continued)

  • Block 5: Motivation statement drafting (65:00-80:00)
  • Block 6: Exit ticket (80:00-90:00)
Module 01 · Nanoscale

Misconceptions to Watch

  • Misconception guardrail: tools generate good questions automatically.
  • Misconception guardrail: a completed connectome is a full explanation of behavior.
  • Misconception guardrail: broad vision statements are sufficient project plans.
  • Misconception guardrail: excitement at the start is enough to carry you through a multi-month project.
Module 01 · Nanoscale

Misconceptions to Watch (continued)

  • Misconception guardrail: if the work feels tedious, you chose the wrong field.
  • Misconception guardrail: good annotators never make errors.
  • Misconception guardrail: my individual contribution is too small to matter.
Module 01 · Nanoscale

Studio Activity

Scenario: Learners produce two artifacts: a question-to-hypothesis sheet and a personal motivation statement. Part A (30 minutes) builds the sheet, Part B (20 minutes) drafts the statement, and a 10-minute peer review closes the session.

Module 01 · Nanoscale

Activity Output Checklist

  • Evidence-linked artifact submitted.
  • At least one limitation or uncertainty stated.
  • Revision point captured from feedback.
Module 01 · Nanoscale

Assessment Rubric

Minimum:

  • Question names organism, region or circuit, and one structural measurement with units.
  • Metric, dataset, and non-claim are all present and consistent with each other.
  • Motivation statement addresses both why and how.
Module 01 · Nanoscale

Assessment Rubric

Strong:

  • Falsification condition names the specific result that would count against the hypothesis.
  • Scope is sized so the first milestone could be finished within a week.
  • Motivation statement names at least two sustainability strategies with triggers ("when X dips, I will Y").
Module 01 · Nanoscale

Assessment Rubric (continued)

  • Non-claim correctly identifies a functional inference the structural data cannot support.
Module 01 · Nanoscale

Assessment Rubric

Failure:

  • Motivational text without measurable outputs, or a question no result could contradict.
  • Motivation statement is generic ("I like brains") or omits a plan for the motivation gap.
  • Claim language exceeds the evidence class of the proposed measurement.
Module 01 · Nanoscale

Exit Ticket

Write a 3-sentence hypothesis with one metric and one caveat. Then write 2 sentences explaining why this question matters to you personally.

Module 01 · Nanoscale

References (Instructor)

  • Use module references listed on the module page.
Module 01 · Nanoscale

Teaching Materials

  • Module page: /modules/module01/
  • Session kit: /teaching/sessions/module01/
  • Worksheet: /assets/worksheets/module01/module01-activity.md
Module 01 · Nanoscale

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Module 01 · Nanoscale

Further teaching detail from the module: **Technical:** define target measurement before tool choice. A well-formed connectomics question specifies the circuit, the organism, the resolution, and the expected structural readout (e.g., synapse count, path length, motif frequency). Tools like FlyWire or CAVE are powerful but directionless without a hypothesis.

Block 1: Opening hook (00:00-12:00) Instructor script: "Welcome. Today we answer one question: why would anyone spend years mapping brain wires? Let me show you." Play 3-minute clip from Sebastian Seung's TED talk. Then show a before/after of a raw EM image vs. a fully reconstructed neuron. Ask: "What questions could you answer with this reconstruction that you could not answer with the raw image?" Collect 3-4 responses on whiteboard. Highlight that each response implies a different measurement. Block 2: Connectomics landscape (12:00-28:00) Instructor script: "Let's ground this in real projects." Walk through three case studies in 5 minutes each: C. elegans (White et al., 1986): the first complete connectome. 302 neurons. What it enabled, what it could not explain. FlyWire whole-brain (Dorkenwald et al., 2024): 130,000+ neurons, 287 proofreaders, first whole-brain connectome of an adult animal with complex behavior. MouseConnects HI-MC (ongoing): scaling to the mouse hippocampus at 10 mm³, the challenge of petascale data. After each case study, ask: "What question drove this project?" Write answers on board. Block 3: Question framing workshop (28:00-48:00) Instructor script: "Now it is your turn. Take 5 minutes to write down the broadest brain question you care about. Do not filter." (5 min silent writing) "Now narrow: what specific circuit or region relates to your question? What structural measurement would you need?" (5 min revision) Pair-share: partners critique each other's questions using the checklist: Does it specify organism? Region? Measurement? Limitation? (10 min) Block 4: Evidence-boundary critique (48:00-65:00) Instructor script: "Every good connectomics question has a twin: the non-claim. What can your structural data NOT tell you?" Present three example hypotheses and their non-claims. Learners practice writing non-claims for their own questions. Class discussion: collect 3 examples of well-formed question + non-claim pairs. Block 5: Motivation statement drafting (65:00-80:00) Instructor script: "Before we close, I want you to write something personal. Why are you here? Not the resume version --- the real version. What about brains or circuits or data makes you want to do this work? And how will you remind yourself of that reason when the work gets tedious?" Silent writing: 10 minutes. Prompt: "Write 3-5 sentences explaining why you want to work in connectomics and what you will do when motivation dips." Voluntary sharing: 2-3 learners read their statements aloud. Block 6: Exit ticket (80:00-90:00) Submit: (1) your testable question with metric, dataset, and non-claim; (2) your motivation statement. Instructor script: "These two documents are your compass for the rest of the program. We will revisit them in Module 06."