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meiosis-prophase-fish-background-review-deck

Build meiosis prophase telomere/FISH background review deck

Metadata

Statusdone
Assignedagent-1096
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-05-07T18:15:02.320165609+00:00
Started2026-05-07T18:17:00.586560639+00:00
Completed2026-05-07T18:47:46.963561853+00:00
Tagsmeiosis, fish, telomere, background-deck, image-retrieval, review, eval-scheduled
Eval score0.93
└ blocking impact0.95
└ completeness0.91
└ constraint fidelity0.70
└ coordination overhead0.94
└ correctness0.93
└ downstream usability0.96
└ efficiency0.88
└ intent fidelity0.87
└ style adherence0.94

Description

Build a separate review deck of meiosis prophase/telomere biology images using the local brief human_meiosis_prophase_slide_brief.md.

User intent:

  • Do not put these images into the current draft presentation yet.
  • Make a standalone background/review slide deck so Erik can inspect and manually reuse images later.
  • Download prior microscopy/FISH/immunofluorescence images showing telomere positioning and chromosome organization across meiotic prophase stages.
  • Follow the source recommendations and URLs in human_meiosis_prophase_slide_brief.md.

Scope:

  • Use the markdown brief as the primary instruction source.
  • Build a compact deck focused on cellular biology background:
    1. Overview of prophase I stages.
    2. Zygotene bouquet / telomere clustering at nuclear envelope.
    3. Pachytene full synapsis / telomeres dispersed but still NE-attached.
    4. Diplotene SC disassembly / chiasmata / telomere detachment context.
    5. Optional mechanism slide: TERB1/TERB2/MAJIN, SUN1/LINC/KASH5 telomere-NE tether.
    6. Citation/license slide.
  • Prefer human oocyte/spermatocyte images where available; supplement with mouse/zebrafish when the brief says those are the clearest telomere/FISH examples.

Image retrieval guidance:

  • Download images from open-access sources listed in the brief where possible, especially PLOS, Frontiers, Nature Communications, bioRxiv CC-BY, and PMC/open-access sources.
  • Do not use paywalled figures unless they are openly accessible and license/attribution is clear. For paywalled suggestions, create a placeholder/source note instead of downloading.
  • Preserve attribution and license metadata for every image.
  • Prefer direct large image URLs from the brief for PLOS figures.
  • For PMC/Nature/Frontiers pages, download the highest practical resolution figure image available without manual browser interaction.
  • Record exact source URL, article title, figure/panel, license, and attribution line in a manifest TSV.

Design/output guidance:

  • This is a review/reference deck, not a polished draft-talk deck. Prioritize clear image visibility and source traceability.
  • One major image/panel per slide is fine; grouped comparison slides are fine where the brief asks for zygotene vs pachytene side-by-side.
  • Include visible stage labels and concise biological point per slide.
  • Add final source/citation slide.
  • Keep images in a local asset directory so they can be manually copied into future decks.

Deliverables:

  • slides/meiosis-prophase-background/meiotic_telomere_biology_review.pdf
  • slides/meiosis-prophase-background/meiotic_telomere_biology_review.typ or another reproducible deck source.
  • slides/meiosis-prophase-background/assets/ containing downloaded image files.
  • slides/meiosis-prophase-background/image_manifest.tsv with source URL, article, figure/panel, license, attribution, local file, and notes.
  • slides/meiosis-prophase-background/README.md summarizing what was downloaded, what was skipped, and why.

Validation:

  • Deck renders successfully as a PDF.
  • Each downloaded image has a manifest row with URL, citation, license/rights note, and attribution line.
  • Paywalled or unclear-license figures are not silently used; they are either skipped or clearly marked as source-only placeholders.
  • The deck covers zygotene, pachytene, and diplotene/background mechanism at minimum.
  • Images are visible/readable at slide scale.
  • git diff --check passes.

Depends on

Required by

↩ Messages 5 messages (all seen)

  1. #1user2026-05-07T18:27:00.777071571+00:00read
    Update from Erik: treat CC-BY/open licensing as preferred, not required, for this internal scientific review/background deck. We are scientists building a review deck for evaluation and slide-crafting, so do not exclude a scientifically important publicly accessible figure only because it is not CC-BY. Still keep provenance rigorous: do not bypass paywalls or access controls, do not claim CC-BY unless the source says so, and record exact rights/license status in image_manifest.tsv. Suggested rights labels include CC-BY/open license, PMC/free-to-read reuse unclear, publisher-accessible review-use, and source-only placeholder/paywalled. Use non-CC or unclear-license images when scientifically useful, but mark them clearly in the manifest and citation/rights slide. Prioritize telomere/FISH/prophase clarity and attribution over strict CC-BY filtering.
  2. #2meiosis-prophase-fish-background-review-deck2026-05-07T18:28:31.197077074+00:00read
    Acknowledged — I will treat CC-BY as preferred rather than mandatory, add scientifically useful publicly accessible non-CC/unclear-license telomere/FISH material where it improves clarity, and label the exact rights status in the manifest and rights slide.
  3. #3user2026-05-07T18:29:16.925923919+00:00read
    Further clarification from Erik: licensing is not a blocker for this deck. Treat reuse of cited scientific figures in an internal/research presentation and review context as standard practice; do not filter out useful meiosis/telomere/FISH figures because they are not CC-BY. Include the best scientifically informative images, cite the original paper/figure/panel clearly, and keep the manifest/source slide complete. The key requirement is attribution and source traceability, not CC-BY status.
  4. #4user2026-05-07T18:29:26.847786381+00:00read
    Tone clarification from Erik: do not make the licensing/rights discussion weird or prominent in the deck. Use normal scientific practice: cite the paper/figure, keep source traceability in the manifest, and focus the slides on the biology. The rights/license details are background bookkeeping, not a visual or narrative centerpiece.
  5. #5meiosis-prophase-fish-background-review-deck2026-05-07T18:31:48.563429460+00:00read
    Acknowledged — I will keep licensing/provenance details in the manifest and README, remove prominent rights language from the biology slides, and include useful publicly accessible scientific figures with clear paper/figure attribution.

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