scientific-schematics

name	scientific-schematics
description	Generate scientific figures as raster PNG via Codex's native image_gen (collaborating-with-codex bridge). Two roles — (1) design exploration, generating several diverse direction drafts in parallel for the user to pick from; the chosen draft is either used directly (manuscript, slides/PPT rework) or handed to tikz-figures as a replication reference, at the user's choice; (2) final raster output for pictorial figures (lighting/texture/3D/hand-drawn concept art, graphical abstracts) or whenever the user prefers a polished PNG. Codex runs its imagegen-scientific-schematics skill for design and visual review; this skill supplies the writing-side entry point, prompt guidance, and publication checklist. Includes an opt-in pastel modern-ML style preset (ICLR/NeurIPS 2024-2025 airy look) for when the user asks for pastel / modern ML figure styling.
allowed-tools	Read Write Edit Bash
license	MIT license
metadata	{"skill-author":"K-Dense Inc."}

Scientific Schematics and Diagrams

Overview

Scientific schematics turn complex concepts into clear visual representations for publication. Generation is delegated to Codex's built-in image_gen tool through the superpower-writing:collaborating-with-codex bridge. Codex runs its own imagegen-scientific-schematics skill, which wraps image_gen in a figure-design and visual-review protocol.

There is no local image CLI, no OAuth login, and no build step. Claude has no native image tool, so the actual raster generation happens inside Codex. This skill is the writing-side entry point: it decides what figure is needed, writes a strong delegation prompt, hands off to Codex, and verifies the result against publication standards.

How it works:

• You describe the diagram and its hard constraints (labels, arrows, zones, colors).
• Codex generates the image with image_gen, reviews it visually, and iterates.
• Codex saves the final PNG into the manuscript's figures/ directory.
• You verify the saved file and reference it in the paper.

Supported figure modalities for systems papers. This skill covers raster schematics via Codex image_gen. For other modalities choose the right tool: TikZ/pgfplots for in-LaTeX vector graphics that must stay in sync with manuscript styling; matplotlib and seaborn for scripted statistical plots (use superpower-writing:scientific-visualization); plotly for interactive HTML; Inkscape SVG for hand-drawn vector diagrams. Use Codex image_gen for architecture/pipeline/conceptual diagrams where visual polish matters more than editable vector source.

When to Use This Skill

This skill plays two distinct roles. Decide which one applies before invoking.

Role 1 — Design exploration (on demand). When the design direction of a figure is unclear — a novel figure type with no obvious layout, several plausible ways to organize the information, or the user explicitly asks to "explore directions" — use image_gen as a fast divergent sketcher: generate 3 direction drafts in parallel (different layouts / information organization, not color variants), show all three to the user, and let them pick. After picking, the user also chooses the delivery form: use the PNG directly (in the manuscript, or as material for a slides/PPT rework), iterate it to final quality in the same Codex session, or hand it to superpower-writing:tikz-figures as a replication reference (ref.png) for a vector rendition. See "Exploration Mode" below.

Role 2 — Final raster output. When the deliverable is a PNG:

• Illustrative concept art with lighting, texture, 3D rendering, or hand-drawn style
• Photorealistic or semi-realistic scene compositions
• Graphical abstracts with strong pictorial elements
• Any figure where the user prefers a polished PNG over vector source

Routing for everything else: routine structural diagrams with a clear design (architecture diagrams, flowcharts, pipelines, sequence diagrams) default to superpower-writing:tikz-figures — its own two-candidate preview covers the layout choice, and vector source keeps formulas and fonts consistent with the body text. That is a default, not a rule: a high-quality image_gen PNG is a legitimate deliverable whenever the user prefers it. For data plots (CDFs, training curves, ablation bars, speedups, Pareto fronts) use superpower-writing:scientific-visualization instead.

Exploration Mode (Role 1)

1. Write one shared figure brief (components, labels, flow), then derive 3 prompts that differ in layout or information organization — e.g. horizontal pipeline vs layered stack vs central-hero-with-panels. Style/color variants do not count as directions.
2. Dispatch all 3 as parallel background bridge calls in one message (each with run_in_background: true and a distinct output path .writing/figures/explore/<slug>-{a,b,c}.png).
3. When all return, Read the three PNGs, show them to the user, and ask which direction to develop (AskUserQuestion, one option per draft with a one-line layout summary).
4. Ask the user how to develop the chosen draft (same AskUserQuestion or a follow-up):
   • Use the PNG directly — iterate it to final quality in the same Codex session (SESSION_ID continuation), move it to .writing/figures/<slug>.png, reference with \includegraphics. Also the right choice when the user plans a manual slides/PPT rework from it.
   • Vector rendition — hand off to superpower-writing:tikz-figures with the chosen PNG as the replication reference. This satisfies tikz-figures' two-candidate requirement (its 复刻 exemption applies); figure-diff.py SSIM verifies the TikZ rendition against the chosen draft.
5. Keep all drafts under .writing/figures/explore/ until the figure ships — the runner-up directions often get revisited.

Graphical abstracts are OPTIONAL. Systems papers typically do not include one. Generate only when the venue explicitly requests it.

How to Generate a Diagram

Delegate to Codex through the bridge. The bridge script lives at ${CLAUDE_PLUGIN_ROOT}/skills/collaborating-with-codex/scripts/codex_bridge.py.

Mandatory: invoke the bridge via the Bash tool with run_in_background: true. Codex calls block 60–120s; a foreground call freezes the session. See superpower-writing:collaborating-with-codex for the full bridge contract.

python3 "${CLAUDE_PLUGIN_ROOT}/skills/collaborating-with-codex/scripts/codex_bridge.py" \
  --cd "<project_root>" \
  --sandbox workspace-write \
  --PROMPT "Use your imagegen-scientific-schematics skill to generate <enriched diagram \
  description>. Save the final selected PNG to .writing/figures/<slug>.png and report the \
  absolute saved path."

Then:

1. Wait for the background bridge call to return (do not poll — you are notified).
2. Confirm the PNG exists at the reported path and Read it to inspect quality.
3. If a gate fails (misspelled label, broken arrow, crowding), continue the same Codex session with its SESSION_ID and one targeted fix per iteration.
4. Reference the figure in the manuscript with \includegraphics.

Codex saves generated images under ~/.codex/generated_images/<session>/ by default and only copies the selected one into the workspace when the prompt asks. Always give an explicit in-project output path, or the asset is stranded outside the repo.

Failure and Recovery

When delegation does not converge, do not loop indefinitely or fabricate a result — fall back to one of these explicit branches.

• Bridge call fails or times out. If the background call returns a non-zero exit, an error, or no SESSION_ID, retry once as a fresh call (not a session continuation, since no session exists). If the second attempt also fails, stop and report the failure plainly to the user with the bridge's error text; do not invent a saved path or claim an image exists.
• Bridge returns but no PNG at the reported path. Re-read Codex's report for an alternate path (often the ~/.codex/generated_images/ default). If found, move it to the intended .writing/figures/ path. If no image was produced at all, treat it as a failed call and apply the retry-once rule above.
• Labels will not converge. Raster generation can misspell dense text. Allow at most 3 targeted fix iterations in the same session. If a label is still wrong after the third, stop iterating and either hand the draft to superpower-writing:tikz-figures for a vector rendition (where text is exact), or deliver the PNG with a note that the caption must correct the affected label. Endless re-prompting on one label is the failure mode to avoid.
• All 3 exploration drafts rejected. If the user dislikes every direction, do not silently regenerate the same three. Ask (AskUserQuestion) what was wrong — wrong layout family, wrong emphasis, missing component — then derive a new brief from that feedback and dispatch one fresh round. After two full rejected rounds, switch to a direct conversation about the intended structure before spending more generation budget.

Writing the Delegation Prompt

The quality of the figure tracks the quality of the prompt. Prepend these scientific guidelines to the user's diagram description before handing it to Codex.

Visual quality: clean white/light background, high contrast, sharp lines and text, generous spacing, publication-ready, no decorative clutter.

Typography: clear sans-serif fonts (Arial/Helvetica style), consistent sizing, all text horizontal and readable, no overlaps.

Scientific standards: accurate representation, every component labeled, standard notation and symbols, units where applicable, legends/scale bars where appropriate.

Accessibility: colorblind-friendly palette (Okabe-Ito), redundant encoding (shape + color, not color alone), works in grayscale.

Layout: logical flow (left-to-right or top-to-bottom), clear visual hierarchy, balanced composition, no clutter.

No figure numbers: do NOT render "Figure 1", captions, or titles in the image. Numbering and captions are added in LaTeX.

Be specific. "Distributed storage write path: client → API gateway → consensus (Raft) → write-ahead log → memtable → SSTable flush to disk" produces a usable figure; "make a system diagram" does not. State the figure type, every component, the flow direction, the exact labels, and the visual semantics (what each color/shape/arrow style means).

The 6-section prompt contract

For any non-trivial diagram, structure the description handed to Codex as six named sections in this order. A flat one-paragraph prompt produces a generic figure; the named structure forces you to fix the style and spell out every label before generation. Codex's imagegen-scientific-schematics skill expects equivalent structure, so write it explicitly.

1. FRAMING (about 5 lines). "A <style-name>-style technical diagram for a <venue> paper. It should feel <adjectives: clean, authoritative, minimal>." Name the venue (NeurIPS / OSDI / NSDI / SOSP) so the tone matches.
2. VISUAL STYLE (about 20 to 30 lines), the most important section. Describe line quality, fills, corner radius, shadow, arrow weight, typography, and whitespace concretely. Without this block the model defaults to a generic corporate look: rounded blue gradient boxes with drop shadows that scream "stock template". Pick one style and keep it identical across every figure in the paper. For systems / ML papers default to a flat, minimal, light-background style (no gradients, no 3D, thin dark-gray arrows, sans-serif labels inside boxes). For modern ML venues (ICLR / NeurIPS / ICML) a second preset is available — the pastel airy style of 2024-2025 papers: read references/style-pastel-ml.md and use its blocks for VISUAL STYLE and COLOR PALETTE.
3. COLOR PALETTE (about 10 lines). Exact hex codes for every color. Use a colorblind-safe set (Okabe-Ito) and assign one accent per logical group.
4. LAYOUT (50 to 150 lines). Every component, box, and zone with its exact text and spatial arrangement. Be exhaustively specific about positions and grouping.
5. CONNECTIONS (30 to 80 lines). Every arrow individually: source, target, style (solid / dashed), label, and routing direction.
6. CONSTRAINTS (about 10 lines). What NOT to include: no figure number, no caption, no clip art, no 3D, no decorative gradients. Adapt per style.

Two rules govern the whole contract:

• SPELL EXACTLY. Raster generators misspell and rearrange dense text. List every label verbatim and add a literal "SPELL ALL LABELS EXACTLY AS WRITTEN, do not rephrase or abbreviate" line. This is the single most common avoidable defect.
• Always 3 attempts; quality varies between runs. The same prompt yields visibly different quality on each generation. Ask Codex to produce at least three attempts and select the best, rather than accepting the first. This pairs with the at-most-three targeted fix iterations in "Failure and Recovery": three fresh attempts up front, then bounded fixes on the chosen one.

Anti-AI-look color rules

The fastest tell of a machine-generated figure is color overuse. Bake these substitutions into the VISUAL STYLE and COLOR PALETTE sections (this table and the thumbnail vocabulary below adapted from LigphiDonk/academic-figure-generator, MIT):

Avoid	Use instead
4-5 colored background panels	white-dominant + faint grey grouping
Saturated header banner bars	small-caps text labels + thin grey divider
A different fill color per module	white fills, color only on borders
Full-color embedded thumbnails	monochrome or 2-color thumbnails
5+ colors in one figure	at most 3 colors + greys
Rainbows / gradients	flat solid colors

Thumbnail vocabulary

Dense conference figures embed small monochrome visualizations inside module boxes. When writing the LAYOUT section, pull phrases from this table instead of leaving boxes as empty labeled rectangles:

Data type	Prompt phrase
Time series	a small time-series waveform thumbnail
Frequency spectrum	a small frequency spectrum bar chart thumbnail
Attention map	a small monochrome attention heatmap grid thumbnail
Trajectory	a small 3D orbital trajectory curve thumbnail
Probability distribution	a small probability distribution bar chart thumbnail
Decision tree	a small decision tree branching diagram thumbnail
Confusion matrix	a small confusion matrix heatmap thumbnail
Network layer	a small neural network layer diagram thumbnail
Feature vector	a small horizontal feature vector bar visualization
Scatter	a small scatter plot with cluster coloring thumbnail
Receptive field	a progressively larger receptive field grid icon
Convolution kernel	a small convolution filter kernel grid thumbnail
Gradient flow	a small gradient flow direction arrow diagram
Loss curve	a small training loss convergence curve thumbnail
ROC curve	a small ROC curve with AUC shading thumbnail
Image sample	a small example image/photo thumbnail
Point cloud	a small 3D point cloud visualization thumbnail
Spatial heatmap	a small spatial heatmap overlay thumbnail

Prompt Locks for Complex Figures

Two failure modes recur on multi-view figures and have slipped past automated review with passing scores, so they must be prevented in the prompt. Codex's imagegen-scientific-schematics skill enforces equivalent locks, but include them explicitly for any non-trivial figure.

Cross-view consistency. When one conceptual entity (a data layout, a fixed mapping, an enum partition) appears across multiple views, a plain prompt lets the model re-invent its specifics per view, producing internal contradictions. Reserve a block at the top that defines the entity once; later views reference it rather than redefining it:

== CRITICAL CONSISTENCY ==
The contract has exactly 3 PUSH positions: PUSH 1 = variant, PUSH 2 = invariant
(value 0xCC), PUSH 3 = variant. This 1-invariant + 2-variant split must hold in
every view where it appears.

Arrow continuity. "An arrow goes from A, crosses the divider, and reaches B" can render as two disconnected stubs. Mandate single-polyline continuity, and for long spans specify the path geometry, not just the endpoints:

== CRITICAL ARROW CONTINUITY ==
Every arrow must be a single continuous unbroken polyline from its source box to an
arrowhead at its target box. No gaps, breaks, or detached segments. Bends are allowed
at right angles but each bend is one connected joint, not two separate arrows.

Example Delegation Prompts

Distributed system architecture:

Use your imagegen-scientific-schematics skill. Distributed transaction processing pipeline,
left-to-right block diagram. Left: client layer, three application nodes (light blue boxes).
Middle: API gateway (green) routing to a Raft consensus cluster (3 nodes), connected to a
write-ahead log (orange cylinder). Right: storage backend — memtable in RAM (purple) and
SSTables on disk (gray cylinders), with a background compaction thread (red arrow) merging
SSTables. Dashed arrows = async, solid = synchronous. Throughput annotations: 100K ops/sec
at client, 50K ops/sec at consensus. Clean white background, no figure number. Save to
.writing/figures/txn_pipeline.png and report the path.

Transformer architecture:

Use your imagegen-scientific-schematics skill. Transformer encoder-decoder architecture.
Left: encoder stack (input embedding, positional encoding, multi-head self-attention,
add & norm, feed-forward, add & norm). Right: decoder stack (output embedding, positional
encoding, masked self-attention, add & norm, cross-attention from encoder, add & norm,
feed-forward, add & norm, linear & softmax). Dashed line for the cross-attention connection.
Light blue = encoder, light red = decoder. Label all components. No figure number. Save to
.writing/figures/transformer.png and report the path.

LaTeX Integration

1. Include with \includegraphics{figures/<slug>.png} (raster schematics are PNG; \includegraphics accepts PNG directly).
2. Write a thorough caption defining every component and abbreviation.
3. Reference the figure in the narrative with Figure~\ref{fig:...} (use the ~ tie).
4. Keep styling consistent across all figures in the paper.
5. Version-control the delegation prompt alongside the figure so it can be regenerated.

Quick Reference Checklist

Before submitting diagrams, verify:

Visual quality

• No overlapping elements; adequate spacing; clean alignment
• All arrows connect properly to their intended targets (no broken stubs)

Information density (opt-in — dense ML-figure styles, not the minimal systems default)

• Every module box has sub-content (sub-boxes, thumbnails, formulas) — no empty placeholder boxes
• At least half the modules embed a small monochrome thumbnail
• Dimensions annotated along main data-flow arrows (e.g. R^(N×D))

Accessibility

• Colorblind-safe palette (Okabe-Ito); works in grayscale; sufficient contrast
• Redundant encoding where appropriate (shapes + colors)

Typography and readability

• Text legible at final size; all elements labeled; consistent fonts
• No text overlaps or cutoffs; units included where applicable
• Labels spelled exactly as required (raster generation can misspell dense text)

Publication standards

• No figure number or caption baked into the image
• Consistent styling with other figures; comprehensive caption written in LaTeX
• Referenced in text; meets venue dimension requirements

Documentation and version control

• Delegation prompt saved for future regeneration
• Git commit includes prompt and output image

Final integration check

• Figure displays correctly in the compiled manuscript
• \ref{} resolves to the correct figure number
• Caption appears on the correct page relative to the figure

Resources and References

• references/best_practices.md — publication standards, file formats, accessibility, and typography guidelines (backend-agnostic).
• references/style-pastel-ml.md — opt-in pastel modern-ML style preset (ICLR/NeurIPS 2024-2025 airy look): style rules, palettes, prompt blocks, element vocabulary, and its own quality checklist.

Publication standards

• Nature Figure Guidelines: https://www.nature.com/nature/for-authors/final-submission
• Science Figure Guidelines: https://www.science.org/content/page/instructions-preparing-initial-manuscript
• IEEE Graphics Guidelines: https://www.ieee.org/publications/reviewers/graphics.html

Integration with Other Skills

• Figure rhetoric (design judgment). Before generating, decide whether the paper needs this figure and which kind. The three-figure storytelling model (motivated example / solution overview / results), the three Figure-1 paradigms with their avoid-conditions, and the design rituals (30-second test, real entities only, one running example throughout) live in tikz-figures/references/figure-rhetoric.md. Read it when the figure is a Figure-1 or solution-overview candidate; it is venue-agnostic across our figure skills.
• superpower-writing:tikz-figures — structural vector diagrams compiled with LaTeX; the default route for paper figures.
• superpower-writing:collaborating-with-codex — the bridge this skill delegates to.
• superpower-writing:scientific-visualization — data plots (matplotlib/seaborn/plotly).
• Drafting / Methods — the architecture-overview figure is a first-class drafting task.
• Peer review — evaluate diagram clarity and accessibility.

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Use this skill to produce clear, accessible, publication-quality diagrams. Generation runs on Codex image_gen with its own visual-review loop; your job is a precise delegation prompt and a verification pass against the checklist above.