Audit batch 1: triage 23 high-confidence reviewed papers

discovery/approve.py

@@ -29,6 +29,7 @@
     "science": "Science",
     "methods": "Methods",
     "software": "Software",
+    "analysis_pipeline": "Analysis Pipeline",
     "tool_paper": "Tool Paper",
     "review": "Review",
     "opinion": "Opinion",

discovery_config.yaml

@@ -21,12 +21,12 @@ seed_papers:
 # Tools: what to look for in paper full text.
 # Each tool has a canonical name (used in BibTeX component field) and aliases.
 tools:
-  - name: "UCLA Miniscope v4"
+  - name: "Miniscope V4"
     aliases:
       - "Miniscope v4"
       - "open-source miniscope"
       - "miniature microscope"
-    wiki_project: "UCLA Miniscope v4"
+    wiki_project: "Miniscope V4"
   - name: "MiniLFOV"
     aliases:
       - "Miniscope-LFOV"

pipeline/reviewed/abdelfattah_2022_neurophotonic.yaml → pipeline/approved/abdelfattah_2022_neurophotonic.yaml

@@ -210,8 +210,12 @@ analysis:
       efforts for measurement and manipulation of brain structure and function"'
     assessment: The paper is a BRAIN Initiative status report that catalogs neurophotonic
       tools including head-mounted miniature microscopes.
-  paper_type: review
-  suggested_project: UCLA Miniscope v4
+  paper_type: Review
+  suggested_project: Miniscope V3
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
+  - Freely-Behaving
   suggested_technique: null
   reasoning: This is a large multi-author (70+) review/status report published in
     Neurophotonics as part of the BRAIN Initiative reporting. Full-text analysis via
@@ -223,7 +227,7 @@ analysis:
     The paper does not cite seed paper DOIs directly in the PMC full text, but mentions
     the UCLA Miniscope by name. Confidence is 0.82 based on confirmed full-text tool
     mentions in a review context.
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:26.373784+00:00'
@@ -235,3 +239,10 @@ stage_history:
   timestamp: '2026-04-11T00:00:00+00:00'
   action: re-analyzed_by_agent_with_fulltext
   result: accepted_review_paper
+- stage: reviewed
+  timestamp: '2026-05-12T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage. Per curator (project lead), the
+    review showcases Miniscope V3 specifically — substantive enough to include
+    (vs. Backhaus/Bagramyan which only namedropped the scope). Project set to
+    Miniscope V3; paper_type kept as Review (BRAIN Initiative status report).

pipeline/reviewed/aharoni_2018_all.yaml → pipeline/approved/aharoni_2018_all.yaml

@@ -51,17 +51,25 @@ analysis:
     most widely disseminated and used tools in neuroscience'
   - 'Miniscopes have provided a base platform for advancements such as miniature light-field
     microscopes, head-mounted wide-field macroscopes, and wire-free microscopes'
-  paper_type: review
-  suggested_project: UCLA Miniscope v4
+  paper_type: Review
+  suggested_project: Miniscope V3
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
+  - Freely-Behaving
+  - Wire-Free
   suggested_technique: calcium imaging
   reasoning: This is a review/perspective article in Nature Methods authored by Daniel
     Aharoni (creator of the UCLA Miniscope) and colleagues from UCLA. The paper extensively
     discusses the UCLA Miniscope platform, its development history, open-source philosophy,
     widespread adoption (450+ labs), and future directions for miniaturized microscopy.
     It is a core publication from the tool developers' lab that reviews the entire
-    field of miniature microscopy with the UCLA Miniscope as a central focus.
+    field of miniature microscopy with the UCLA Miniscope as a central focus. Tagged
+    as Miniscope V3 (curator override) since v4 postdates this 2018 paper.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:43.317785+00:00'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'

pipeline/reviewed/aharoni_2019_circuit.yaml → pipeline/approved/aharoni_2019_circuit.yaml

@@ -43,8 +43,13 @@ analysis:
   - "As part of the UCLA Miniscope project"
   - "Making use of the UCLA Miniscope imaging and data"
   - "An MLA was implemented in a reconfigured UCLA Miniscope"
-  paper_type: review
-  suggested_project: UCLA Miniscope v4
+  paper_type: Review
+  suggested_project: Miniscope V3
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
+  - Wire-Free
+  - Freely-Behaving
   suggested_technique: calcium imaging
   reasoning: >-
     This is a review paper authored by Daniel Aharoni (UCLA Miniscope project lead)
@@ -55,9 +60,14 @@ analysis:
     wide-field/volumetric imaging capabilities. This is a core tool paper from
     the project developers themselves.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:43.317696+00:00'
 - stage: reviewed
   timestamp: '2026-04-10'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage; project corrected to Miniscope V3
+    (pre-v4 era); keywords added.

pipeline/reviewed/ajabi_2023_population.yaml → pipeline/approved/ajabi_2023_population.yaml

@@ -45,8 +45,12 @@ analysis:
   - "calcium videos were recorded with a miniscope (v3; https://miniscope.org) containing a monochrome CMOS imaging sensor (MT9V032C12STM, ON Semiconductor) connected to a custom data acquisition (DAQ) box (https://miniscope.org)"
   - "controlled using Miniscope custom acquisition software (https://miniscope.org)"
   - "Aharoni for advice and assistance with the UCLA miniscope"
-  paper_type: science
-  suggested_project: UCLA Miniscope v4
+  paper_type: Science
+  suggested_project: Miniscope V3, Miniscope DAQ
+  suggested_keywords:
+  - Calcium Imaging
+  - Freely-Behaving
+  - Spatial Navigation
   suggested_technique: calcium imaging
   reasoning: >-
     This paper uses the UCLA Miniscope (v3) and Miniscope DAQ hardware as the primary
@@ -56,9 +60,14 @@ analysis:
     the device used is actually a v3 (predecessor to v4), it is part of the UCLA Miniscope
     family and the paper clearly uses the tool for its core research.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:43.318877+00:00'
 - stage: reviewed
   timestamp: '2026-04-10T00:00:00+00:00'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage; project set to Miniscope V3 +
+    Miniscope DAQ per explicit v3 callout in methods; keywords added.

pipeline/reviewed/arac_2019_deepbehavior.yaml → pipeline/approved/arac_2019_deepbehavior.yaml

@@ -48,14 +48,24 @@ analysis:
   - social interaction test in freely moving mice with simultaneous miniscope calcium
     imaging
   - one of them wearing a miniaturized microscope
-  paper_type: software
-  suggested_project: UCLA Miniscope v4
+  paper_type: Software
+  suggested_project: Miniscope V3
+  suggested_keywords:
+  - Calcium Imaging
+  - Freely-Behaving
+  - Social Behavior
   suggested_technique: calcium imaging; behavior analysis
   reasoning: DeepBehavior toolbox demonstrates tracking mice during social interaction
     where one mouse wears a UCLA Miniscope for simultaneous calcium imaging. Senior
     author Peyman Golshani is from the UCLA Miniscope development group.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:43.318141+00:00'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage. Software paper from Golshani lab
+    (DeepBehavior toolbox) — miniscope use is a demo application; tagged Miniscope
+    V3 (pre-v4 era). DeepBehavior itself left out of vocab for now.

pipeline/reviewed/asaoka_2025_dissociable.yaml → pipeline/approved/asaoka_2025_dissociable.yaml

@@ -48,8 +48,12 @@ analysis:
     and background fluorescence, motion correction and source separation"
   - "Following the MiniAn pipeline, output values of Ca2+ activity were normalized"
   - "described at http://Miniscope.org"
-  paper_type: science
-  suggested_project: UCLA Miniscope v4;Miniscope DAQ;Minian
+  paper_type: Science
+  suggested_project: Miniscope V4, Miniscope DAQ, Minian
+  suggested_keywords:
+  - Calcium Imaging
+  - Freely-Behaving
+  - Prefrontal Cortex
   suggested_technique: calcium imaging
   reasoning: This paper uses the UCLA Miniscope v4 (version 4.4) for in vivo calcium
     imaging of prefrontal cortex neurons during decision-making and habitual behavior
@@ -58,7 +62,12 @@ analysis:
     motion correction, and source separation via CNMF. The paper directly uses three
     tools from the Miniscope ecosystem.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:43.326390+00:00'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage; project list comma-normalized;
+    keywords added.

pipeline/reviewed/bai_2023_learningprolonged.yaml → pipeline/approved/bai_2023_learningprolonged.yaml

@@ -50,23 +50,35 @@ analysis:
   - 'Author keyword: "miniscope Ca(2+) imaging"'
   - 'Abstract: "Deep-brain calcium imaging shows that the peak of trace activity in
     the CA1 and subiculum is extended toward the US"'
-  paper_type: science
-  suggested_project: UCLA Miniscope v4
+  paper_type: Science
+  suggested_project: Miniscope V4, Miniscope DAQ
+  suggested_keywords:
+  - Calcium Imaging
+  - Freely-Behaving
+  - Fear & Anxiety
+  - Memory
+  - Hippocampus
   suggested_technique: deep-brain calcium imaging
   reasoning: >-
     Paper uses miniscope calcium imaging for deep-brain recordings in CA1 and
     subiculum during trace fear conditioning in freely moving mice. The authors
     explicitly list "miniscope Ca(2+) imaging" as a keyword. The paper cites seed
     paper Cai et al. 2016 (doi:10.1038/nature17955), a foundational UCLA Miniscope
-    paper. The research is from Chinese Academy of Sciences (external lab). No full
-    text was available in PMC, but the author-provided keyword "miniscope Ca(2+)
-    imaging" is strong direct evidence of tool usage. Confidence is 0.90 rather than
-    higher because without full text we cannot confirm the exact miniscope model
-    (v3 vs v4), though v4 is most likely given the 2023 publication date.
+    paper. The research is from Chinese Academy of Sciences (external lab). Methods
+    section labels the scope "UCLA V2, LabMaker" — per curator (project lead),
+    this is a LABmaker-side labeling artifact and the actual hardware is the UCLA
+    Miniscope V4. Acquisition via MiniScopeControl + Miniscope DAQ.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:43.320990+00:00'
 - stage: reviewed
   timestamp: '2026-04-11T00:00:00+00:00'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: 'Approved during high-confidence triage. Paper labels miniscope "UCLA
+    V2, LabMaker" in methods, but per curator (project lead) this is a LABmaker
+    labeling artifact — actual scope is UCLA Miniscope V4. Project: Miniscope V4 +
+    Miniscope DAQ. Keywords added.'

pipeline/reviewed/beacher_2021_circuit.yaml → pipeline/approved/beacher_2021_circuit.yaml

@@ -58,8 +58,15 @@ analysis:
     and future"
   - "miniscope imaging is a fantastic tool to identify underlying neurobiological functions
     of SI and SUD"
-  paper_type: review
-  suggested_project: UCLA Miniscope v4
+  paper_type: Review
+  suggested_project: null   # ecosystem-adjacent: field review, no specific scope used
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
+  - Freely-Behaving
+  - Wire-Free
+  - Social Behavior
+  - Reward
   suggested_technique: calcium imaging
   reasoning: This is a mini-review paper that extensively discusses and advocates the
     use of open-source miniscopes for studying social interaction (SI) and substance
@@ -68,10 +75,16 @@ analysis:
     and discusses wire-free miniscopes, motorized commutators, and other miniscope
     hardware advances. The paper reviews how miniscopes enable deep brain calcium imaging
     in freely behaving animals and advocates their use for SI and SUD research.
-related_to_project: true
-stage: reviewed
+  related_to_project: true
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:26.374316+00:00'
 - stage: reviewed
   timestamp: '2026-04-11'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage. Field-review paper; project left
+    empty (ecosystem-adjacent). Keywords added. Fixed indentation of related_to_project
+    (was at top level, moved under analysis).

pipeline/reviewed/beacher_2024_modular.yaml → pipeline/approved/beacher_2024_modular.yaml

@@ -56,8 +56,13 @@ analysis:
   - "The modifiable nature of the operant chamber enables simultaneous multidimensional behavioral recordings and in vivo neural recordings such as 1-photon calcium imaging using miniscopes"
   - "optimized to support long-term miniscope in vivo imaging in rats while also mitigating many potentially detrimental risks"
   - "one such benefit provided by long term housing is to prolong the life of miniscope equipment"
-  paper_type: methods
-  suggested_project: UCLA Miniscope v4
+  paper_type: Methods
+  suggested_project: null   # ecosystem-adjacent: describes operant chamber for any miniscope, not a specific project
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
+  - Freely-Behaving
+  - Chronic Imaging
   suggested_technique: calcium imaging
   reasoning: >-
     This paper presents "The Miniscope Box," an open-source operant chamber specifically
@@ -72,9 +77,15 @@ analysis:
     form factor. This is a clear methods paper that develops complementary hardware for
     miniscope-based experiments.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:47.019392+00:00'
 - stage: reviewed
   timestamp: '2026-04-11'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage. Operant-chamber methods paper;
+    project left empty (ecosystem-adjacent — not tied to a specific project).
+    paper_type kept as Methods (MethodsX journal). Keywords added.

pipeline/reviewed/beacher_2025_miniscope.yaml → pipeline/approved/beacher_2025_miniscope.yaml

@@ -66,8 +66,13 @@ analysis:
     based on open‐source robotic surgical instruments previously used for mice"
   - "The combined virus injection and GRIN lens implantation surgery would work identically
     for UCLA, Inscopix, and other open‐source miniscopes"
-  paper_type: methods
-  suggested_project: UCLA Miniscope v4
+  paper_type: Protocol
+  suggested_project: Miniscope V4
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
+  - Freely-Behaving
+  - Reward
   suggested_technique: calcium imaging
   reasoning: This is a detailed methods/protocol paper published in Current Protocols
     that provides step-by-step instructions for miniscope calcium imaging in freely
@@ -78,9 +83,17 @@ analysis:
     and cites the MiniLFOV seed paper (Guo et al.). The paper is strongly related
     as a methods protocol for the miniscope ecosystem.
   related_to_project: true
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:47.019401+00:00'
 - stage: reviewed
   timestamp: '2026-04-11'
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: 'Approved during high-confidence triage. Paper uses Barbera miniscope_v2.0
+    fork (custom variant), not directly a tracked project, but uses Miniscope V4
+    baseplate from LABmaker — tagged as Miniscope V4 on that basis. paper_type
+    corrected from methods → Protocol (Current Protocols journal). MiniLFOV
+    reference is parallel/applicability, not actual use.'

pipeline/reviewed/dong_2022_minian.yaml → pipeline/approved/dong_2022_minian.yaml

@@ -79,8 +79,11 @@ analysis:
     text: Daniel Aharoni is a co-author
     note: Paper is from the Miniscope project team. Tool developer papers must not
       be rejected.
-  paper_type: software
+  paper_type: Analysis Pipeline
   suggested_project: Minian
+  suggested_keywords:
+  - Open-Source
+  - Calcium Imaging
   suggested_technique: calcium imaging analysis
   reasoning: This paper introduces Minian, which is explicitly listed as one of the
     Miniscope project's tools in discovery_config.yaml. Minian is an open-source
@@ -90,7 +93,7 @@ analysis:
     rejected per the analysis rules. The paper describes the software's architecture,
     validation, and interactive visualization features. Confidence is 0.99 as this
     is unambiguously a core project tool paper.
-stage: reviewed
+stage: approved
 stage_history:
 - stage: candidate
   timestamp: '2026-04-11T03:20:26.373490+00:00'
@@ -103,3 +106,8 @@ stage_history:
   timestamp: '2026-04-10T00:00:00+00:00'
   agent: citation-analysis-agent
   reason: Minian is a listed project tool; paper introduces it; authored by tool developers
+- stage: reviewed
+  timestamp: '2026-05-11T00:00:00+00:00'
+  agent: curator
+  reason: Approved during high-confidence triage; paper_type set to Analysis Pipeline
+    (new vocab entry); keywords added.