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Reproducibility and FAIR Principles in Connectomics

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Contents · 19 slides
  1. 1. Reproducibility and FAIR Principles in Connectomics
  2. 2. Learning Objectives
  3. 3. Capability Target
  4. 4. Concept Focus
  5. 5. Core Workflow
  6. 6. Core Workflow (continued)
  7. 7. Run of Show (60 min)
  8. 8. Run of Show (60 min) (continued)
  9. 9. Misconceptions to Watch
  10. 10. Studio Activity
  11. 11. Activity Output Checklist
  12. 12. Assessment Rubric
  13. 13. Assessment Rubric
  14. 14. Assessment Rubric (continued)
  15. 15. Assessment Rubric
  16. 16. Exit Ticket
  17. 17. References (Instructor)
  18. 18. Teaching Materials
  19. 19. Read, review, or teach

Slide 1 of 19

H01 electron microscopy with object segmentation and original 2 µm scale bar Nanoscale · Module 21

Reproducibility and FAIR Principles in Connectomics

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

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Learning Objectives

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Capability Target

Publish a reproducibility-ready connectomics package (data + methods + metadata + limitations) that an external group can audit and reuse.

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Concept Focus

1) FAIR as implementation checklist

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Core Workflow

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Core Workflow (continued)

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Run of Show (60 min)

Figure description and teaching notes

Pre-class preparation (15 min async)
Bring one analysis you have run, in whatever state it is in. It does not need to be tidy; untidy is more useful here.
Read Technical Unit 04, section 2, on materialization versions and root-ID instability.
Minute-by-minute plan

00:00-06:00 | Framing: the silent bug
Prompt: "Your notebook ran fine last month and gives a different number today. Nothing in your code changed. What happened?"
Establish that analysis against an unpinned segmentation is the most common silent correctness failure in this field.

06:00-16:00 | The five-element checklist, modeled
Instructor walks one real analysis through: dataset release ID, materialization number, code commit hash, environment specification, parameter configuration.
Show what breaks when each one is missing, in turn.

16:00-30:00 | Guided practice: audit your own work
Learners score their brought-in analysis against the five elements. Most will fail two or three; say so in advance to make that safe.
Produce a remediation list ordered by how cheap each fix is.

30:00-40:00 | Clean-environment rerun
Attempt a rerun of a partner's analysis from their instructions alone, without asking them questions.
Log every point of friction. The friction log is the deliverable, not the successful rerun.

40:00-50:00 | Known limitations, written honestly
Each learner drafts a limitations paragraph naming concrete failure modes, excluded samples, and failed runs — not generic caveats.
Discuss why this is a hidden-curriculum norm: reviewers expect it, and almost nobody is taught to write it.

50:00-57:00 | Competency check
Submit: completed five-element record, friction report on a partner's package, and one limitations paragraph.

57:00-60:00 | Exit ticket
"One thing in my current work that another person could not reproduce today."
Formative checkpoints
At 30 minutes: every learner has identified at least one missing element in their own work. A learner reporting five out of five has probably not audited honestly — check.
At 50 minutes: limitations paragraphs name specific failure modes rather than generic hedges.

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Run of Show (60 min) (continued)

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Misconceptions to Watch

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Studio Activity

Scenario: Your lab plans to release a connectomics analysis package to collaborators.

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Activity Output Checklist

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Assessment Rubric

Minimum pass

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Assessment Rubric

Strong performance

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Assessment Rubric (continued)

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Assessment Rubric

Common failure modes

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Exit Ticket

Take one prior analysis output and add:

  1. provenance metadata,
  2. reproducibility instructions,
  3. a 5-line limitations section.

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References (Instructor)

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Teaching Materials

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Read, review, or teach

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