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docs(cadecon): align tutorials with convergence / palette / fit-mode changes#165

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docs/tutorial-alignment
Jul 8, 2026
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docs(cadecon): align tutorials with convergence / palette / fit-mode changes#165
daharoni merged 1 commit into
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docs/tutorial-alignment

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@daharoni daharoni commented Jul 8, 2026

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Final item of the pre-publication review series: bring the in-app CaDecon tutorials in line with the behavior shipped in #153–163. Content + figure-color changes only — verified with tsc -b apps/cadecon, eslint, and prettier.

What changed

Theory — "How does CaDecon know when to stop?" (03-theory.ts step 11)
The step carried an explicit NOTE that the stop criterion was "still being finalized." It's now finalized, so I removed the note and rewrote the description to match: convergence is judged in kernel shape space — stability of the rise-to-peak time and FWHM — declared after several consecutive stable iterations, with the reported kernel = the median (consensus) of the last few iterates (which is also what guards against late drift). Mentions the Convergence Tolerance control.

Convergence panel tabs (01-basics.ts step 7, 04-interpreting.ts step 2)
Both described tabs that no longer exist ("Threshold", "Spike Eff."). Rewrote them against the real ConvergencePanel tabs — Asymptote / Kernel / Distributions:

  • Basics leads with the Asymptote dashboard (the four signals that should flatten: kernel shape, kernel-fit R², PVE, activity stability).
  • Interpreting uses Asymptote as the first health check and notes the convergence marker; per-cell alpha/PVE/event-rate now correctly attributed to the Distributions tab.

Kernel quality (04-interpreting.ts step 3)
Documents the new degenerate-fit warning (⚠ n/N fits degenerate, from the #162 FitMode work) as a cue to raise coverage or re-tile.

Theory figures (theory-figures.ts)
Now draw with the shared colorblind-safe Okabe-Ito palette imported from @calab/ui/chart (spikes → bluish-green, cutoff → orange, kernel → reddish-purple, dropped → neutral grey) instead of the old D3 category10 green/orange — making the "match the dashboard palette" comment actually true.

Verification

  • tsc -b apps/cadecon clean (confirms the new @calab/ui/chart import resolves).
  • eslint + prettier clean.
  • Static-only; I did not spin up the browser for this one — happy to Playwright-verify the theory figure render on request.

🤖 Generated with Claude Code

…changes

Tutorial-content pass so the in-app tutorials match the behavior shipped
during the review series (#153-163). Verified: typecheck, eslint, prettier.

- Theory tutorial "How does CaDecon know when to stop?" (03-theory step 11):
  removed the stale NOTE (the stop criterion is now finalized) and rewrote it
  to describe shape-space convergence — stability of the kernel's peak time and
  FWHM, several consecutive stable iterations (patience), and the reported
  kernel as the median-of-last-few-iterates consensus. Points at the
  Convergence Tolerance control.
- Convergence panel steps now match the real ConvergencePanel tabs
  (Asymptote / Kernel / Distributions): basics step 7 leads with the Asymptote
  dashboard (the four signals that flatten); interpreting step 2 uses it as the
  first health check and drops the non-existent "Threshold" signal.
- Interpreting step 3 documents the new degenerate-fit warning as a
  kernel-quality cue.
- theory-figures.ts now draws with the shared colorblind-safe Okabe-Ito palette
  (imported from @calab/ui/chart) instead of the old D3 category10 green/orange,
  making the "match the dashboard palette" comment true.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
@daharoni daharoni merged commit 269ad0f into main Jul 8, 2026
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@daharoni daharoni deleted the docs/tutorial-alignment branch July 8, 2026 22:54
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