journal-club-slides

Use when building journal club or literature-report slides from research PDFs and you need a figure-first, audience-facing, visually polished deck that preserves paper logic, keeps crops safe, pairs main and supporting evidence correctly, and passes render-based QA.

Overview

Use this skill to turn one or more research-paper PDFs into presentation-ready journal club or literature-report slides.

The standard is not "extract paper content into PPT". The standard is to produce a deck that is:

• faithful to the paper's argument
• optimized for live speaking
• visually strong enough to present directly
• figure-first rather than text-first
• grounded in real main and supporting evidence
• verified in rendered output, not just in source form

This skill is intentionally strict because paper decks often fail in predictable ways: wrong figure pairing, unsafe crops, unreadable support images, creator-facing labels, visually weak layouts, or a .pptx that looks fine in source but breaks after render.

When to Use

Use this skill when the user wants:

• a journal club, lab meeting, literature review, or paper-report deck from one or more PDFs
• slide structure that follows the paper's logic rather than generic summary templates
• large readable figures with bilingual or audience-facing explanation
• visually polished academic slides rather than rough screenshot collages
• support figures mapped to the same conclusion as the main figure
• final delivery that is checked through real render QA

Do not use this as the primary workflow for:

• teaching decks that need major textbook-style pedagogy beyond the paper itself
• simple abstract-only summaries with no figure work
• business or corporate decks where paper-figure integrity is not the central constraint

Quality Bar: What Good Output Looks Like

A good output from this skill has all of the following:

• the narrative follows the original paper's reasoning chain
• each result slide answers a clear question or states a clear conclusion
• figures are complete, undistorted, and readable
• main figures and same-conclusion support figures are paired correctly
• slide text speaks to the audience, not to the deck author
• the visual style is clean, premium, academic, and presentation-safe
• the final deck survives export/render QA without broken fonts, clipped headers, or unreadable support panels

Hard Requirements

1. Preserve the paper's logic

• Follow the original argument order, especially the Results sequence.
• Do not reorder results just to make the layout prettier.
• If multiple papers are combined, build one integrated storyline instead of stacking mini-decks.

2. Use question-driven or claim-driven result slides

• Prefer a question or direct claim as the title of each result slide.
• Every result slide should make it obvious what problem that page is answering.
• Titles should help a speaker move naturally through the talk.

3. Figure integrity comes before decoration

• Prefer complete safe figure crops before panel splitting.
• Never crop into panel letters, axes titles, tick labels, legends, color bars, scale bars, workflow endpoints, right-edge labels, or bottom labels.
• If unsure, leave slightly more margin rather than cutting content.
• Never stretch figures; preserve aspect ratio at placement time.

4. Main + support evidence must be paired correctly

• Main figure and same-conclusion supporting figure should appear on the same slide whenever feasible.
• They should be shown at comparable visual scale, not as a hero image plus tiny thumbnail.
• Support pairing must come from conclusion-level mapping using the paper text and legends, not page adjacency.
• Never use a nearby text-heavy paper page as a fake support image.

5. Real support figures beat prose substitutes

• Always check whether supplementary figures exist in the same PDF or in separate supplementary files.
• If real supplementary figure assets exist, use them.
• If the page is dense, crop the actual supplementary figure body safely instead of shrinking a full text-heavy page to unreadability.
• Only use a support-summary text box when true support image assets genuinely cannot be obtained.

6. Slides must be audience-facing

• Write for listeners, not for the slide author.
• Remove creator-facing labels such as: Take-home, Reading note, Interpretation, speaker hint, "this slide wants to show", or similar scaffolding.
• If bilingual wording is requested, titles and explanatory text should both respect that request.
• Explanations should state what the figure shows, why it matters, and how it advances the paper's logic.

7. Visual design must be strong, restrained, and readable

• Prefer white or near-white content pages unless the user requests otherwise.
• Aim for premium academic / science-tech styling rather than business-template polish.
• Increase figure footprint before shrinking figures.
• Use hierarchy, spacing, alignment, restrained accent colors, and subtle structure rather than heavy shadows or decorative frames.
• Avoid oversized rounded cards, thick borders, bottom decorative bars, and dashboard-like chrome around figures.
• Make the deck feel presentation-ready, not merely correct.

8. Live-speaking readability is mandatory

• Use large enough titles and explanatory text for projection.
• Favor fuller layouts with clear hierarchy over sparse layouts with tiny figures.
• If a figure pair is too dense to read on one slide, split the content rather than shrinking it into illegibility.
• If support evidence remains unreadable at slide scale, re-crop or redesign the support area.

9. Render-based QA is non-optional

• .pptx source generation is not final acceptance.
• Final acceptance requires export/render inspection when the environment allows it.
• Verify crop integrity, figure identity, support readability, font rendering, title overflow, and audience-facing text in the rendered output.

Recommended Deck Structure

A common paper-report flow is:

1. Cover
2. Why the problem matters
3. What question the paper asks
4. Why this team can do the work 5+. Results slides in paper order
5. Strengths / limitations / implications
6. Summary

Adapt this structure to the paper type:

• experimental papers: results-driven progression
• review papers: framework / field tension / conceptual map / future directions
• multi-paper synthesis: one integrated storyline with explicit transitions

Workflow

Step 1. Build a paper workspace

Create a project folder containing:

• original PDF(s)
• extracted text
• rendered page images
• supplementary page images
• crops
• PPT generation scripts
• rendered QA outputs

Keep assets organized enough that figure identity can be audited later.

Step 2. Extract both text and page images

Work on two tracks in parallel:

• text track: abstract, introduction/problem framing, results, figure legends, supplementary legends
• image track: rendered paper pages for crop work and visual figure verification

If dependencies are missing, prefer a local virtual environment over assuming global installs.

Step 3. Map questions, figures, and support evidence

Before slide design, explicitly map:

• each major figure
• the question or claim it answers
• which supplementary or extended-data figure supports the same conclusion
• where that result sits in the paper's logic

Do this before layout. Good decks are built from argument mapping, not from dragging images onto slides.

Step 4. Write slide logic before layout

For each results slide, define:

• the title question or direct claim
• what the main figure proves
• what the support figure validates
• the most important quantitative or conceptual takeaway
• how this slide bridges from the previous one

Step 5. Extract figures conservatively

• Start with full-figure-safe crops.
• For dense Nature/Cell/Science-style pages, remove dead page margin first, not scientific content.
• Confirm visually that the crop is figure-dominant rather than mostly body text.
• For review/framework papers, verify that the crop is a real figure body, not a text-heavy page with minor illustration.

Step 6. Design slides for clarity and impact

Preferred result-slide behavior:

• main figure and support figure on the same page where feasible
• similar visual weight for main and support evidence
• concise audience-facing explanatory text
• clean figure area with minimal framing
• a clear visual center on each slide

Useful layout patterns include:

• left main figure / right support + explanation
• top figure pair / bottom conclusion strip
• two-up figure comparison with a compact text panel

But layout should always follow readability and argument structure, not a rigid template.

Step 7. Polish for presentation quality

Actively improve:

• title hierarchy
• page fullness without clutter
• bilingual readability if needed
• scientific premium feel
• rhythm across slides
• cover / background / summary slides so the deck has visual presence, not just competent internals

For stronger aesthetics:

• use restrained accent colors
• create one visual center per slide
• trim dense text before adding decorative structure
• rebalance blank areas rather than letting figures stay too small

Step 8. Run render QA

Export to PDF and/or slide images when possible. Check for:

• clipped titles or header-band overflow
• tofu boxes / garbled CJK / broken fonts
• unreadable support panels
• wrong figure-number-to-image mapping
• creator-facing labels left in place
• image distortion
• accidental decorative leftovers
• blank panels created by late edits or language fallback

Step 9. Fix and re-render

Do not stop at the first generated deck. If render QA reveals problems, patch the source, regenerate, and re-check. At least one fix-and-verify loop is expected for serious paper decks.

Special Cases

Review or framework-heavy papers

• Do not force them into a results-only format.
• Prioritize conceptual figures, framework diagrams, field maps, and future-direction logic.
• If a concept figure is dense, it may deserve two slides: one for structure, one for implications.

Multi-paper decks

• Do not present them as isolated mini-presentations.
• Build a single narrative with explicit transitions and a shared biological or conceptual question.
• Exclude unrelated papers even if they were attached nearby.

Environment or font constraints

• If bilingual rendering fails because CJK fonts are missing, treat that as a blocker, not a cosmetic issue.
• Prefer fixing the font/render environment first.
• If a fallback is unavoidable, make it deliberate and complete; do not leave a half-bilingual broken deck.

Common Pitfalls

1. Using a summary card instead of the real support figure when supplementary assets exist.
2. Pairing support figures by page proximity instead of by conclusion.
3. Declaring a crop safe before checking the rendered slide.
4. Stretching figures by forcing both height and width.
5. Leaving support panels so small that they are technically present but presentation-useless.
6. Keeping creator-facing labels in the final deck.
7. Making the deck structurally correct but visually weak.
8. Using too much dashboard-style framing around scientific figures.
9. Treating source .pptx success as final QA.
10. Failing to adapt the workflow for review papers or multi-paper synthesis.

Portability Rules

To keep this skill usable across environments and users:

• describe workflows in terms of outcomes and checks, not one narrow project layout
• prefer broadly available tooling and local-venv fallback patterns
• do not assume a specific font stack, filesystem, or user path
• make rendered verification part of the process whenever the environment allows it
• keep paper-specific lessons as references, but preserve a general workflow in the main skill
• when renaming or publishing a local umbrella skill under a new outward-facing name, migrate or recreate every referenced support file before calling the published skill complete
• after a rename, verify that every file listed in ## References actually exists under the new skill directory rather than only in the old one

Delivery Checklist

Before calling the deck done, confirm:

• output PPT path is known
• render QA output path is known when available
• figure/support mapping is correct
• crops preserve scientific content
• support figures are readable enough to matter
• slide text is audience-facing
• visual style is clean and presentation-ready
• no obvious decorative over-framing remains
• the delivered deck is the intended final variant, not an exploratory one

References

• references/metaedit-jcslides-mapping-and-crop-notes.md
• references/multi-paper-plasmid-copy-number-deck.md
• references/python-pptx-render-qa-first-pass.md
• references/figure-integrity-deep-fix-notes.md