From c3d7c24776d4c24700251d9832017035c63c34e8 Mon Sep 17 00:00:00 2001 From: daharoni Date: Tue, 12 May 2026 02:21:00 +0200 Subject: [PATCH] Audit batch 1: triage 23 high-confidence reviewed papers MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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references: 2023_biosensor_a - Preprint of an already-approved peer-reviewed paper: ajabi_2021_population (superseded by Nature 2023 version) Vocabulary changes (vocabulary.yaml): - Renamed `UCLA Miniscope v4` → `Miniscope V4` (drop UCLA prefix for cleaner wiki page name).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) --- discovery/approve.py | 1 + discovery_config.yaml | 4 +- .../abdelfattah_2022_neurophotonic.yaml | 17 +- .../aharoni_2018_all.yaml | 16 +- .../aharoni_2019_circuit.yaml | 16 +- .../ajabi_2023_population.yaml | 15 +- .../arac_2019_deepbehavior.yaml | 16 +- .../asaoka_2025_dissociable.yaml | 15 +- .../bai_2023_learningprolonged.yaml | 28 ++- .../beacher_2021_circuit.yaml | 21 +- .../beacher_2024_modular.yaml | 17 +- .../beacher_2025_miniscope.yaml | 19 +- .../dong_2022_minian.yaml | 12 +- .../madruga_2025_opensource.yaml | 14 +- .../2021_neuroinfoviewer.yaml | 9 +- .../2023_biosensor_a.yaml | 9 +- .../ajabi_2021_population.yaml | 9 +- .../backhaus_2023_alloptical.yaml | 9 +- .../bagramyan_2020_lightweight.yaml | 8 +- .../bao_2024_accurate.yaml | 8 +- .../{reviewed => rejected}/baowan_2025.yaml | 9 +- .../barbera_2020_opensource.yaml | 8 +- .../barbera_2022_miniature.yaml | 9 +- .../battivelli_2024_how.yaml | 11 +- .../benisty_2022_review.yaml | 8 +- references.bib | 197 ++++++++++++++++++ vocabulary.yaml | 24 ++- 27 files changed, 472 insertions(+), 57 deletions(-) rename pipeline/{reviewed => approved}/abdelfattah_2022_neurophotonic.yaml (93%) rename pipeline/{reviewed => approved}/aharoni_2018_all.yaml (89%) rename pipeline/{reviewed => approved}/aharoni_2019_circuit.yaml (86%) rename pipeline/{reviewed => approved}/ajabi_2023_population.yaml (85%) rename pipeline/{reviewed => approved}/arac_2019_deepbehavior.yaml (80%) rename pipeline/{reviewed => approved}/asaoka_2025_dissociable.yaml (86%) rename pipeline/{reviewed => approved}/bai_2023_learningprolonged.yaml (72%) rename pipeline/{reviewed => approved}/beacher_2021_circuit.yaml (82%) rename pipeline/{reviewed => approved}/beacher_2024_modular.yaml (85%) rename pipeline/{reviewed => approved}/beacher_2025_miniscope.yaml (84%) rename pipeline/{reviewed => approved}/dong_2022_minian.yaml (92%) rename pipeline/{reviewed => approved}/madruga_2025_opensource.yaml (93%) rename pipeline/{reviewed => rejected}/2021_neuroinfoviewer.yaml (87%) rename pipeline/{reviewed => rejected}/2023_biosensor_a.yaml (90%) rename pipeline/{reviewed => rejected}/ajabi_2021_population.yaml (86%) rename pipeline/{reviewed => rejected}/backhaus_2023_alloptical.yaml (88%) rename pipeline/{reviewed => rejected}/bagramyan_2020_lightweight.yaml (88%) rename pipeline/{reviewed => rejected}/bao_2024_accurate.yaml (88%) rename pipeline/{reviewed => rejected}/baowan_2025.yaml (87%) rename pipeline/{reviewed => rejected}/barbera_2020_opensource.yaml (88%) rename pipeline/{reviewed => rejected}/barbera_2022_miniature.yaml (88%) rename pipeline/{reviewed => rejected}/battivelli_2024_how.yaml (85%) rename pipeline/{reviewed => rejected}/benisty_2022_review.yaml (88%) diff --git a/discovery/approve.py b/discovery/approve.py index e1843e1..ce05e3d 100644 --- a/discovery/approve.py +++ b/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", diff --git a/discovery_config.yaml b/discovery_config.yaml index fa3bc12..b88fcad 100644 --- a/discovery_config.yaml +++ b/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" diff --git a/pipeline/reviewed/abdelfattah_2022_neurophotonic.yaml b/pipeline/approved/abdelfattah_2022_neurophotonic.yaml similarity index 93% rename from pipeline/reviewed/abdelfattah_2022_neurophotonic.yaml rename to pipeline/approved/abdelfattah_2022_neurophotonic.yaml index 742fa99..169c238 100644 --- a/pipeline/reviewed/abdelfattah_2022_neurophotonic.yaml +++ b/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). diff --git a/pipeline/reviewed/aharoni_2018_all.yaml b/pipeline/approved/aharoni_2018_all.yaml similarity index 89% rename from pipeline/reviewed/aharoni_2018_all.yaml rename to pipeline/approved/aharoni_2018_all.yaml index 4ad53ae..0d920a7 100644 --- a/pipeline/reviewed/aharoni_2018_all.yaml +++ b/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' diff --git a/pipeline/reviewed/aharoni_2019_circuit.yaml b/pipeline/approved/aharoni_2019_circuit.yaml similarity index 86% rename from pipeline/reviewed/aharoni_2019_circuit.yaml rename to pipeline/approved/aharoni_2019_circuit.yaml index cc7d8e7..06f4697 100644 --- a/pipeline/reviewed/aharoni_2019_circuit.yaml +++ b/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. diff --git a/pipeline/reviewed/ajabi_2023_population.yaml b/pipeline/approved/ajabi_2023_population.yaml similarity index 85% rename from pipeline/reviewed/ajabi_2023_population.yaml rename to pipeline/approved/ajabi_2023_population.yaml index b6a5931..3ff25bc 100644 --- a/pipeline/reviewed/ajabi_2023_population.yaml +++ b/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. diff --git a/pipeline/reviewed/arac_2019_deepbehavior.yaml b/pipeline/approved/arac_2019_deepbehavior.yaml similarity index 80% rename from pipeline/reviewed/arac_2019_deepbehavior.yaml rename to pipeline/approved/arac_2019_deepbehavior.yaml index 000fd73..cf6cabe 100644 --- a/pipeline/reviewed/arac_2019_deepbehavior.yaml +++ b/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. diff --git a/pipeline/reviewed/asaoka_2025_dissociable.yaml b/pipeline/approved/asaoka_2025_dissociable.yaml similarity index 86% rename from pipeline/reviewed/asaoka_2025_dissociable.yaml rename to pipeline/approved/asaoka_2025_dissociable.yaml index 81689bb..b8c522d 100644 --- a/pipeline/reviewed/asaoka_2025_dissociable.yaml +++ b/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. diff --git a/pipeline/reviewed/bai_2023_learningprolonged.yaml b/pipeline/approved/bai_2023_learningprolonged.yaml similarity index 72% rename from pipeline/reviewed/bai_2023_learningprolonged.yaml rename to pipeline/approved/bai_2023_learningprolonged.yaml index a947492..41daac5 100644 --- a/pipeline/reviewed/bai_2023_learningprolonged.yaml +++ b/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.' diff --git a/pipeline/reviewed/beacher_2021_circuit.yaml b/pipeline/approved/beacher_2021_circuit.yaml similarity index 82% rename from pipeline/reviewed/beacher_2021_circuit.yaml rename to pipeline/approved/beacher_2021_circuit.yaml index aadff2b..1ee1bba 100644 --- a/pipeline/reviewed/beacher_2021_circuit.yaml +++ b/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). diff --git a/pipeline/reviewed/beacher_2024_modular.yaml b/pipeline/approved/beacher_2024_modular.yaml similarity index 85% rename from pipeline/reviewed/beacher_2024_modular.yaml rename to pipeline/approved/beacher_2024_modular.yaml index dcea2db..1dc55ed 100644 --- a/pipeline/reviewed/beacher_2024_modular.yaml +++ b/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. diff --git a/pipeline/reviewed/beacher_2025_miniscope.yaml b/pipeline/approved/beacher_2025_miniscope.yaml similarity index 84% rename from pipeline/reviewed/beacher_2025_miniscope.yaml rename to pipeline/approved/beacher_2025_miniscope.yaml index 4f45d9d..829cdee 100644 --- a/pipeline/reviewed/beacher_2025_miniscope.yaml +++ b/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.' diff --git a/pipeline/reviewed/dong_2022_minian.yaml b/pipeline/approved/dong_2022_minian.yaml similarity index 92% rename from pipeline/reviewed/dong_2022_minian.yaml rename to pipeline/approved/dong_2022_minian.yaml index fe03bc8..683664b 100644 --- a/pipeline/reviewed/dong_2022_minian.yaml +++ b/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. diff --git a/pipeline/reviewed/madruga_2025_opensource.yaml b/pipeline/approved/madruga_2025_opensource.yaml similarity index 93% rename from pipeline/reviewed/madruga_2025_opensource.yaml rename to pipeline/approved/madruga_2025_opensource.yaml index 1ff577c..e79df77 100644 --- a/pipeline/reviewed/madruga_2025_opensource.yaml +++ b/pipeline/approved/madruga_2025_opensource.yaml @@ -78,8 +78,14 @@ analysis: Guo et al. MiniLFOV 2023 (ref 7)' note: References multiple Miniscope family papers as foundational 1P work that motivated this 2P system. - paper_type: tool_paper + paper_type: Tool Paper suggested_project: UCLA 2P Miniscope + suggested_keywords: + - Open-Source + - Two-Photon + - Calcium Imaging + - Freely-Behaving + - Hippocampus suggested_technique: two-photon calcium imaging reasoning: This paper introduces the UCLA 2P Miniscope, which is explicitly listed as a tracked tool in discovery_config.yaml. It is authored by the Miniscope project's @@ -88,7 +94,7 @@ analysis: microscope, demonstrating calcium imaging in hippocampal CA1, retrosplenial cortex dendrites, and dentate gyrus at depths over 620 um. As a tool paper that introduces a tracked instrument in the Miniscope family, it is clearly related to the project. -stage: reviewed +stage: approved stage_history: - stage: candidate timestamp: '2026-04-11T03:20:26.374449+00:00' @@ -102,3 +108,7 @@ stage_history: agent: citation-analysis-agent reason: 'Tool paper introducing UCLA 2P Miniscope, a tracked tool in the Miniscope family. From the tool developers'' lab (Aharoni/Golshani). Related: true.' +- stage: reviewed + timestamp: '2026-05-11T00:00:00+00:00' + agent: curator + reason: Approved during high-confidence triage; added keywords from vocabulary. diff --git a/pipeline/reviewed/2021_neuroinfoviewer.yaml b/pipeline/rejected/2021_neuroinfoviewer.yaml similarity index 87% rename from pipeline/reviewed/2021_neuroinfoviewer.yaml rename to pipeline/rejected/2021_neuroinfoviewer.yaml index 0935581..92d6b30 100644 --- a/pipeline/reviewed/2021_neuroinfoviewer.yaml +++ b/pipeline/rejected/2021_neuroinfoviewer.yaml @@ -63,7 +63,7 @@ analysis: Unpaywall, CrossRef). The paper is closed access with no OA copy. Confidence is capped well below 0.5 due to absence of both abstract and full text. Manual review with full text access is recommended. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:26.374829+00:00' @@ -72,3 +72,10 @@ stage_history: agent: citation-analysis-agent note: 'Marked needs_fulltext: no abstract or full text available. Title and seed paper citation suggest UCLA Miniscope usage but cannot confirm with direct quotes.' +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Title suggests miniscope analysis + software, but no full text available to determine whether this is an + ecosystem-extending tool (processes our scope's output) or a competing analysis + tool. 0.35 confidence too low to approve without verification. diff --git a/pipeline/reviewed/2023_biosensor_a.yaml b/pipeline/rejected/2023_biosensor_a.yaml similarity index 90% rename from pipeline/reviewed/2023_biosensor_a.yaml rename to pipeline/rejected/2023_biosensor_a.yaml index 3408c21..d9de4ed 100644 --- a/pipeline/reviewed/2023_biosensor_a.yaml +++ b/pipeline/rejected/2023_biosensor_a.yaml @@ -60,7 +60,7 @@ analysis: the MiniLFOV as a key enabling technology for the next stage of their biosensor system development. This constitutes a meaningful tool connection beyond mere scientific context citation.' -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:47.019723+00:00' @@ -70,3 +70,10 @@ stage_history: - stage: reviewed timestamp: '2026-04-11T00:00:00+00:00' reason: Full-text analysis found explicit MiniLFOV reference as proposed future tool +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Paper proposes MiniLFOV as future + direction to make their biosensor portable but does not currently use any of our + tools — too peripheral. Same precedent as backhaus_2023, bagramyan_2020, + barbera_2022. diff --git a/pipeline/reviewed/ajabi_2021_population.yaml b/pipeline/rejected/ajabi_2021_population.yaml similarity index 86% rename from pipeline/reviewed/ajabi_2021_population.yaml rename to pipeline/rejected/ajabi_2021_population.yaml index 9b17d84..5e80df7 100644 --- a/pipeline/reviewed/ajabi_2021_population.yaml +++ b/pipeline/rejected/ajabi_2021_population.yaml @@ -57,9 +57,16 @@ analysis: strong evidence of tool usage. Confidence is 0.85 rather than higher because the full text could not be fully parsed (PDF binary) so the exact methods sentence naming the device could not be directly quoted. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:43.323595+00:00' - stage: reviewed timestamp: '2026-04-10' +- stage: reviewed + timestamp: '2026-05-11T00:00:00+00:00' + agent: curator + reason: Rejected as duplicate. This bioRxiv preprint (2021) was superseded by the + peer-reviewed Nature 2023 version (doi 10.1038/s41586-023-05813-2, already + approved as ajabi_2023_population). Policy — prefer peer-reviewed publication + over preprint when both exist. diff --git a/pipeline/reviewed/backhaus_2023_alloptical.yaml b/pipeline/rejected/backhaus_2023_alloptical.yaml similarity index 88% rename from pipeline/reviewed/backhaus_2023_alloptical.yaml rename to pipeline/rejected/backhaus_2023_alloptical.yaml index da58a76..a1fbbf1 100644 --- a/pipeline/reviewed/backhaus_2023_alloptical.yaml +++ b/pipeline/rejected/backhaus_2023_alloptical.yaml @@ -63,7 +63,14 @@ analysis: in detail. Confidence is 0.82 rather than higher because the paper covers a broad range of optical methods and the Miniscope discussion is one component of the larger chapter. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:43.322709+00:00' +- stage: reviewed + timestamp: '2026-05-11T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Book chapter on all-optical + physiology methods mentions UCLA Miniscope-v4 as one of several open-source + 1P options but does not substantively engage with the tool — too peripheral + to include. diff --git a/pipeline/reviewed/bagramyan_2020_lightweight.yaml b/pipeline/rejected/bagramyan_2020_lightweight.yaml similarity index 88% rename from pipeline/reviewed/bagramyan_2020_lightweight.yaml rename to pipeline/rejected/bagramyan_2020_lightweight.yaml index 81c937d..7d9c827 100644 --- a/pipeline/reviewed/bagramyan_2020_lightweight.yaml +++ b/pipeline/rejected/bagramyan_2020_lightweight.yaml @@ -54,9 +54,15 @@ analysis: key predecessor. The paper is a methods contribution presenting an alternative miniscope design inspired by and compared against the UCLA Miniscope family. No full text was available for deeper analysis, so confidence is moderated. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:43.322220+00:00' - stage: reviewed timestamp: '2026-04-11' +- stage: reviewed + timestamp: '2026-05-11T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Independent miniscope design from + Bagramyan / Universite Laval — cites Cai 2016 as predecessor context but does + not use any UCLA Miniscope hardware. Not in our project family. diff --git a/pipeline/reviewed/bao_2024_accurate.yaml b/pipeline/rejected/bao_2024_accurate.yaml similarity index 88% rename from pipeline/reviewed/bao_2024_accurate.yaml rename to pipeline/rejected/bao_2024_accurate.yaml index 6238be0..f01b92c 100644 --- a/pipeline/reviewed/bao_2024_accurate.yaml +++ b/pipeline/rejected/bao_2024_accurate.yaml @@ -56,9 +56,15 @@ analysis: acknowledges Minian as a related tool. Confidence is moderate because the connection is indirect -- Minian is cited only in passing as related work, not used or tested against directly. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:43.322793+00:00' - stage: reviewed timestamp: '2026-04-11' +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Competing one-photon segmentation + pipeline (SUNS2-ANE) — cites Minian once in related-work but does not benchmark + against or use it. Same precedent as competing-tool rejections. diff --git a/pipeline/reviewed/baowan_2025.yaml b/pipeline/rejected/baowan_2025.yaml similarity index 87% rename from pipeline/reviewed/baowan_2025.yaml rename to pipeline/rejected/baowan_2025.yaml index 52607a2..013f28c 100644 --- a/pipeline/reviewed/baowan_2025.yaml +++ b/pipeline/rejected/baowan_2025.yaml @@ -61,9 +61,16 @@ analysis: tool mentions. Confidence is capped at 0.45 due to lack of full text. Marked as related because a review of miniature microscopes that cites the Miniscope v4 paper almost certainly discusses the UCLA Miniscope platform. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:26.376422+00:00' - stage: reviewed timestamp: '2026-04-11' +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Chinese-language invited review on + head-mounted miniature microscopes — almost certainly discusses UCLA Miniscope + by topic, but no full text or abstract available to verify depth of engagement. + Rejected as too uncertain. diff --git a/pipeline/reviewed/barbera_2020_opensource.yaml b/pipeline/rejected/barbera_2020_opensource.yaml similarity index 88% rename from pipeline/reviewed/barbera_2020_opensource.yaml rename to pipeline/rejected/barbera_2020_opensource.yaml index 203e3ef..063c365 100644 --- a/pipeline/reviewed/barbera_2020_opensource.yaml +++ b/pipeline/rejected/barbera_2020_opensource.yaml @@ -62,9 +62,15 @@ analysis: extension that builds on the Miniscope DAQ platform for behavioral measurement, not merely a passing citation. related_to_project: true -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:43.321302+00:00' - stage: reviewed timestamp: '2026-04-11' +- stage: reviewed + timestamp: '2026-05-11T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Per curator (project lead) — the + "miniScope" referenced here is Barbera's own miniscope_v2.0 lineage (Lin lab), + not UCLA Miniscope or UCLA Miniscope DAQ. LLM was misled by the shared name. diff --git a/pipeline/reviewed/barbera_2022_miniature.yaml b/pipeline/rejected/barbera_2022_miniature.yaml similarity index 88% rename from pipeline/reviewed/barbera_2022_miniature.yaml rename to pipeline/rejected/barbera_2022_miniature.yaml index b435e62..ccc4472 100644 --- a/pipeline/reviewed/barbera_2022_miniature.yaml +++ b/pipeline/rejected/barbera_2022_miniature.yaml @@ -67,9 +67,16 @@ analysis: that positions itself relative to the UCLA Miniscope ecosystem. Confidence is moderate (0.75) because while it substantively references and compares against the tools, it does not actually use them -- it builds its own independent system. -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:47.019187+00:00' - stage: reviewed timestamp: '2026-04-11' +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Barbera lineage miniature scope + (Lin lab) — competing design that cites and compares against UCLA Miniscope / + MiniLFOV but does not use them. Same precedent as rejected barbera_2020_opensource + and bagramyan_2020_lightweight. diff --git a/pipeline/reviewed/battivelli_2024_how.yaml b/pipeline/rejected/battivelli_2024_how.yaml similarity index 85% rename from pipeline/reviewed/battivelli_2024_how.yaml rename to pipeline/rejected/battivelli_2024_how.yaml index 10fdd72..e57ad81 100644 --- a/pipeline/reviewed/battivelli_2024_how.yaml +++ b/pipeline/rejected/battivelli_2024_how.yaml @@ -59,10 +59,17 @@ analysis: so confidence is capped at 0.45. The paper is from EMBL Rome and Zhejiang University, not the tool developers' lab. The Miniscope citation is likely one among many tools discussed in this broad review rather than a central focus. -related_to_project: true -stage: reviewed + related_to_project: true +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:26.374968+00:00' - stage: reviewed timestamp: '2026-04-11' +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Behavior/ethology review (Nature + Reviews Neuroscience) — cites Shuman 2019 in passing as one of many neural + monitoring tools for freely behaving animals; no substantive engagement. + Fixed indentation of related_to_project (was at top level). diff --git a/pipeline/reviewed/benisty_2022_review.yaml b/pipeline/rejected/benisty_2022_review.yaml similarity index 88% rename from pipeline/reviewed/benisty_2022_review.yaml rename to pipeline/rejected/benisty_2022_review.yaml index 4984d4f..fd59266 100644 --- a/pipeline/reviewed/benisty_2022_review.yaml +++ b/pipeline/rejected/benisty_2022_review.yaml @@ -57,9 +57,15 @@ analysis: is moderate (0.72) because full text was inaccessible for direct quote extraction, but the reference list and topic strongly indicate Miniscope coverage. related_to_project: true -stage: reviewed +stage: rejected stage_history: - stage: candidate timestamp: '2026-04-11T03:20:43.321099+00:00' - stage: reviewed timestamp: '2026-04-13' +- stage: reviewed + timestamp: '2026-05-12T00:00:00+00:00' + agent: curator + reason: Rejected during high-confidence triage. Data-processing review that cites + Cai 2016 + CaImAn but full text was inaccessible — depth of engagement with our + tools unclear. Rejected by default per peripheral-mention precedent. diff --git a/references.bib b/references.bib index f4539f7..88f5104 100644 --- a/references.bib +++ b/references.bib @@ -31,3 +31,200 @@ @article{zhao_2025_minixl volume = {11}, year = {2025} } + +@article{abdelfattah_2022_neurophotonic, + author = {Abdelfattah, Ahmed and Allu, Srinivasa Rao and Campbell, Robert E. and Cheng, Xiaojun and Cižmár, Tomáš and Costantini, Irene and Emiliani, Valentina and Fomin-Thunemann, Natalie and Gilad, Ariel and Fernández Alfonso, Tomás and Ferri, Christopher G. L. and Harris, Andrew and Hillman, Elizabeth M. C. and Holt, Matthew G. and Kiliç, Kivilcim and Miller, Evan W. and Mesquita, Rickson C. and Nadella, K.M. Naga Srinivas and Nägerl, U. Valentin and Perez Campos, Citlali and Puppo, Francesca and Shoham, Shy and Silver, R. Angus and Srinivasan, Vivek J. and Thunemann, Martin and Tian, Lei and Vinogradov, Sergei A. and Vitale, Flavia and Uhlirova, Hana and Xu, Chris and Yang, Mu-Han and Zhao, Yongxin and Ahuja, Sapna and Akkin, Taner and Brake, Joshua and Boas, David A. and Buckley, Erin M. and Chen, Anderson I. and De Vittorio, Massimo and Devor, Anna and Doran, Patrick and El Khatib, Mirna and Fainman, Yeshaiahu and Han, Xue and Hochgeschwender, Ute and Ji, Na and Lake, Evelyn and Li, Lei and Li, Tianqi and Machler, Philipp and Nasu, Yusuke and Nimmerjahn, Axel and Ondrácková, Petra and Pavone, Francesco S. and Peterka, Darcy and Pisano, Filippo and Pisanello, Ferruccio and Sabatini, Bernardo L. and Sadegh, Sanaz and Sakadžic, Sava and Shroff, Sanaya N. and Sims, Ruth R. and Smith, Spencer LaVere and Tian, Lin and Troxler, Thomas and Valera, Antoine and Vaziri, Alipasha and Wang, Lihong V. and Yang, Changhuei and Yellen, Gary and Yizhar, Ofer}, + doi = {10.1117/1.nph.9.s1.013001}, + issn = {2329-423X}, + journal = {Neurophotonics}, + keywords = {Open-Source, Calcium Imaging, Freely-Behaving}, + month = {April}, + number = {S1}, + paper_type = {Review}, + project = {Miniscope V3}, + publisher = {SPIE-Intl Soc Optical Eng}, + title = {Neurophotonic Tools for Microscopic Measurements and Manipulation: Status Report}, + url = {http://dx.doi.org/10.1117/1.nph.9.s1.013001}, + volume = {9}, + year = {2022} +} + +@article{aharoni_2018_all, + author = {Aharoni, Daniel and Khakh, Baljit S. and Silva, Alcino J. and Golshani, Peyman}, + doi = {10.1038/s41592-018-0266-x}, + issn = {1548-7105}, + journal = {Nature Methods}, + keywords = {Open-Source, Calcium Imaging, Freely-Behaving, Wire-Free}, + month = {December}, + number = {1}, + pages = {11–13}, + paper_type = {Review}, + project = {Miniscope V3}, + publisher = {Springer Science and Business Media LLC}, + title = {All the light that we can see: a new era in miniaturized microscopy}, + url = {http://dx.doi.org/10.1038/s41592-018-0266-x}, + volume = {16}, + year = {2018} +} + +@article{aharoni_2019_circuit, + author = {Aharoni, Daniel and Hoogland, Tycho M.}, + doi = {10.3389/fncel.2019.00141}, + issn = {1662-5102}, + journal = {Frontiers in Cellular Neuroscience}, + keywords = {Open-Source, Calcium Imaging, Wire-Free, Freely-Behaving}, + month = {April}, + paper_type = {Review}, + project = {Miniscope V3}, + publisher = {Frontiers Media SA}, + title = {Circuit Investigations With Open-Source Miniaturized Microscopes: Past, Present and Future}, + url = {http://dx.doi.org/10.3389/fncel.2019.00141}, + volume = {13}, + year = {2019} +} + +@article{ajabi_2023_population, + author = {Ajabi, Zaki and Keinath, Alexandra T. and Wei, Xue-Xin and Brandon, Mark P.}, + doi = {10.1038/s41586-023-05813-2}, + issn = {1476-4687}, + journal = {Nature}, + keywords = {Calcium Imaging, Freely-Behaving, Spatial Navigation}, + month = {March}, + number = {7954}, + pages = {892–899}, + paper_type = {Science}, + project = {Miniscope V3, Miniscope DAQ}, + publisher = {Springer Science and Business Media LLC}, + title = {Population dynamics of head-direction neurons during drift and reorientation}, + url = {http://dx.doi.org/10.1038/s41586-023-05813-2}, + volume = {615}, + year = {2023} +} + +@article{arac_2019_deepbehavior, + author = {Arac, Ahmet and Zhao, Pingping and Dobkin, Bruce H. and Carmichael, S. Thomas and Golshani, Peyman}, + doi = {10.3389/fnsys.2019.00020}, + issn = {1662-5137}, + journal = {Frontiers in Systems Neuroscience}, + keywords = {Calcium Imaging, Freely-Behaving, Social Behavior}, + month = {May}, + paper_type = {Software}, + project = {Miniscope V3}, + publisher = {Frontiers Media SA}, + title = {DeepBehavior: A Deep Learning Toolbox for Automated Analysis of Animal and Human Behavior Imaging Data}, + url = {http://dx.doi.org/10.3389/fnsys.2019.00020}, + volume = {13}, + year = {2019} +} + +@article{asaoka_2025_dissociable, + author = {Asaoka, Nozomi and Pagano, Diane and Hayashi, Yasunori}, + doi = {10.1101/2025.05.19.654900}, + keywords = {Calcium Imaging, Freely-Behaving, Prefrontal Cortex}, + month = {May}, + paper_type = {Science}, + project = {Miniscope V4, Miniscope DAQ, Minian}, + publisher = {openRxiv}, + title = {Dissociable roles of prefrontal plasticity in decision making strategy and execution of habitual behavior}, + url = {http://dx.doi.org/10.1101/2025.05.19.654900}, + year = {2025} +} + +@article{bai_2023_learningprolonged, + author = {Bai, Tao and Zhan, Lijie and Zhang, Na and Lin, Feikai and Saur, Dieter and Xu, Chun}, + doi = {10.1016/j.celrep.2023.112853}, + issn = {2211-1247}, + journal = {Cell Reports}, + keywords = {Calcium Imaging, Freely-Behaving, Fear & Anxiety, Memory, Hippocampus}, + month = {August}, + number = {8}, + pages = {112853}, + paper_type = {Science}, + project = {Miniscope V4, Miniscope DAQ}, + publisher = {Elsevier BV}, + title = {Learning-prolonged maintenance of stimulus information in CA1 and subiculum during trace fear conditioning}, + url = {http://dx.doi.org/10.1016/j.celrep.2023.112853}, + volume = {42}, + year = {2023} +} + +@article{beacher_2021_circuit, + author = {Beacher, Nicholas J. and Washington, Kayden A. and Werner, Craig T. and Zhang, Yan and Barbera, Giovanni and Li, Yun and Lin, Da-Ting}, + doi = {10.3389/fncir.2021.762441}, + issn = {1662-5110}, + journal = {Frontiers in Neural Circuits}, + keywords = {Open-Source, Calcium Imaging, Freely-Behaving, Wire-Free, Social Behavior, Reward}, + month = {October}, + paper_type = {Review}, + publisher = {Frontiers Media SA}, + title = {Circuit Investigation of Social Interaction and Substance Use Disorder Using Miniscopes}, + url = {http://dx.doi.org/10.3389/fncir.2021.762441}, + volume = {15}, + year = {2021} +} + +@article{beacher_2024_modular, + author = {Beacher, Nicholas J. and Kuo, Jessica Y. and Targum, Miranda and Wang, Michael and Washington, Kayden A. and Barbera, Giovanna and Lin, Da-Ting}, + doi = {10.1016/j.mex.2024.102721}, + issn = {2215-0161}, + journal = {MethodsX}, + keywords = {Open-Source, Calcium Imaging, Freely-Behaving, Chronic Imaging}, + month = {June}, + pages = {102721}, + paper_type = {Methods}, + publisher = {Elsevier BV}, + title = {A modular, cost-effective, versatile, open-source operant box solution for long-term miniscope imaging, 3D tracking, and deep learning behavioral analysis}, + url = {http://dx.doi.org/10.1016/j.mex.2024.102721}, + volume = {12}, + year = {2024} +} + +@article{beacher_2025_miniscope, + author = {Beacher, Nicholas J. and Wang, Michael W. and Broomer, Matthew C. and Kuo, Jessica Y. and Washington, Kayden A. and Targum, Miranda and Zhang, Yan and Barbera, Giovanni and Lin, Da‐Ting}, + doi = {10.1002/cpz1.70090}, + issn = {2691-1299}, + journal = {Current Protocols}, + keywords = {Open-Source, Calcium Imaging, Freely-Behaving, Reward}, + month = {January}, + number = {1}, + paper_type = {Protocol}, + project = {Miniscope V4}, + publisher = {Wiley}, + title = {Miniscope Imaging of Nucleus Accumbens Neural Activity in Freely Behaving Rats: Virus Injection, Gradient Index Lens Implantation, Recording Strategies, and Analytical Methods}, + url = {http://dx.doi.org/10.1002/cpz1.70090}, + volume = {5}, + year = {2025} +} + +@article{dong_2022_minian, + author = {Dong, Zhe and Mau, William and Feng, Yu and Pennington, Zachary T and Chen, Lingxuan and Zaki, Yosif and Rajan, Kanaka and Shuman, Tristan and Aharoni, Daniel and Cai, Denise J}, + doi = {10.7554/elife.70661}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {Open-Source, Calcium Imaging}, + month = {June}, + paper_type = {Analysis Pipeline}, + project = {Minian}, + publisher = {eLife Sciences Publications, Ltd}, + title = {Minian, an open-source miniscope analysis pipeline}, + url = {http://dx.doi.org/10.7554/elife.70661}, + volume = {11}, + year = {2022} +} + +@article{madruga_2025_opensource, + author = {Madruga, Blake A. and Dorian, Conor C. and Yang, Long and Sehgal, Megha and Silva, Alcino J. and Shtrahman, Matthew and Aharoni, Daniel and Golshani, Peyman}, + doi = {10.1038/s41467-025-62534-y}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {Open-Source, Two-Photon, Calcium Imaging, Freely-Behaving, Hippocampus}, + month = {August}, + number = {1}, + paper_type = {Tool Paper}, + project = {UCLA 2P Miniscope}, + publisher = {Springer Science and Business Media LLC}, + title = {Open-source, high performance miniature 2-photon microscopy systems for freely behaving animals}, + url = {http://dx.doi.org/10.1038/s41467-025-62534-y}, + volume = {16}, + year = {2025} +} diff --git a/vocabulary.yaml b/vocabulary.yaml index 61501a4..71baf4d 100644 --- a/vocabulary.yaml +++ b/vocabulary.yaml @@ -26,7 +26,8 @@ # the aliases there to detect tool mentions, then maps to the canonical # `name` here for the BibTeX field. projects: - - name: "UCLA Miniscope v4" + - name: "Miniscope V3" + - name: "Miniscope V4" - name: "MiniLFOV" - name: "MiniXL" - name: "Minian" @@ -45,6 +46,8 @@ paper_types: description: "Paper extending or developing methodology" - name: "Software" description: "Software or analysis pipeline paper" + - name: "Analysis Pipeline" + description: "Data-processing / analysis pipeline paper (e.g. miniscope analysis pipelines, cell segmentation pipelines)" - name: "Tool Paper" description: "Introduces a new tool in the project family" - name: "Review" @@ -104,4 +107,21 @@ keywords: # # The maintainer reviews periodically. Promoted entries move into the # appropriate list above; rejected entries are deleted from this section. -pending_suggestions: [] +pending_suggestions: + - target: "keywords" + name: "Nucleus Accumbens" + proposed_by: "curator" + rationale: "Major reward/motivation recording target; appears in protocol papers + and reward/decision-making studies. Parallel to existing Hippocampus / Prefrontal + Cortex / Amygdala entries." + example_dois: + - "10.1002/cpz1.70090" # beacher_2025_miniscope + proposed_date: "2026-05-11" + - target: "keywords" + name: "Anterior Thalamus" + proposed_by: "curator" + rationale: "Head-direction cell recording target; comes up in HD-cell papers + from Brandon, Taube, etc. Likely recurs across multiple papers in the corpus." + example_dois: + - "10.1038/s41586-023-05813-2" # ajabi_2023_population + proposed_date: "2026-05-11"