Audit batch 1: triage 23 high-confidence reviewed papers#19
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Triaged the high-confidence tier of pipeline/reviewed/ (≥0.35
confidence, 23 papers). Approved 12 and rejected 11; merged the 12
into references.bib (now 14 entries total including the 2 seed
papers).
Approved (12):
aharoni_2018_all, aharoni_2019_circuit, ajabi_2023_population,
arac_2019_deepbehavior, asaoka_2025_dissociable, bai_2023_learningprolonged,
beacher_2021_circuit, beacher_2024_modular, beacher_2025_miniscope,
dong_2022_minian, madruga_2025_opensource, abdelfattah_2022_neurophotonic
Rejected (11):
- Competing-tool / non-UCLA-lineage scopes: barbera_2020_opensource,
barbera_2022_miniature, bagramyan_2020_lightweight
- Reviews that only namedrop our tools without substantive
engagement: backhaus_2023_alloptical, baowan_2025,
battivelli_2024_how, benisty_2022_review
- Competing analysis tools: bao_2024_accurate, 2021_neuroinfoviewer
- Future-direction-only references: 2023_biosensor_a
- Preprint of an already-approved peer-reviewed paper:
ajabi_2021_population (superseded by Nature 2023 version)
Vocabulary changes (vocabulary.yaml):
- Renamed `UCLA Miniscope v4` → `Miniscope V4` (drop UCLA prefix
for cleaner wiki page name).
- Added `Miniscope V3` for older papers (Aharoni 2018/2019,
Abdelfattah 2022, Arac 2019, Ajabi 2023).
- Added paper_type `Analysis Pipeline` for Minian-style processing
pipeline papers (distinct from general `Software`).
- Seeded pending_suggestions with two brain-region keyword
candidates surfaced during triage: Nucleus Accumbens
(beacher_2025_miniscope), Anterior Thalamus (ajabi_2023_population).
Code:
- discovery_config.yaml: tool entry for Miniscope V4 renamed in
parallel with the vocab change.
- discovery/approve.py: added `analysis_pipeline → Analysis Pipeline`
mapping to _PAPER_TYPE_CANONICAL.
Policy decisions captured during triage (so future batches stay
consistent):
- Ecosystem-adjacent papers (e.g. operant chamber, field reviews
that don't use a specific scope): leave `project` blank rather
than forcing a tag. Two papers in this batch fit (beacher_2021,
beacher_2024).
- Multi-tool papers: comma-separate the project list (e.g.
`Miniscope V4, Miniscope DAQ, Minian` for asaoka_2025).
- Prefer peer-reviewed publication over preprint when both exist.
- Per-paper version corrections noted in YAML reasoning: many
pre-v4-era papers had been auto-tagged v4 by the LLM and were
corrected to V3 during curator review.
The SchemaSync `Has_paper_type` enum on the wiki side needs a parallel
`Analysis Pipeline` addition; tracking separately.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Contributor
Citations Summary
Added (12)
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Triaged the high-confidence tier of
pipeline/reviewed/(≥0.35 confidence, 23 papers). Approved 12 and rejected 11; merged the 12 intoreferences.bib(now 14 entries total including the 2 seed papers).Approved (12)
Rejected (11)
barbera_2020_opensource,barbera_2022_miniature,bagramyan_2020_lightweightbackhaus_2023_alloptical,baowan_2025,battivelli_2024_how,benisty_2022_reviewbao_2024_accurate,2021_neuroinfoviewer2023_biosensor_aajabi_2021_population(Nature 2023 version is in the approved list above)Each rejected YAML has a
curatorentry instage_historyexplaining the reasoning.Vocabulary changes (
vocabulary.yaml)UCLA Miniscope v4→Miniscope V4(drop UCLA prefix for cleaner wiki page name)Miniscope V3for older papers (Aharoni 2018/2019, Abdelfattah 2022, Arac 2019, Ajabi 2023)Analysis Pipelinefor Minian-style processing pipeline papers (distinct from generalSoftware)pending_suggestionswith two brain-region keyword candidates surfaced during triage: Nucleus Accumbens (beacher_2025) and Anterior Thalamus (ajabi_2023)Policy decisions captured during triage
(so future batches stay consistent)
projectblank rather than forcing a tag. Two papers in this batch fit (beacher_2021, beacher_2024).Miniscope V4, Miniscope DAQ, Minianfor asaoka_2025).Follow-up
The SchemaSync
Has_paper_typeenum on the wiki side needs a parallelAnalysis Pipelineaddition — opening a PR there next.🤖 Generated with Claude Code