diff --git a/discovery/fulltext.py b/discovery/fulltext.py
index c57ae86..21a972b 100644
--- a/discovery/fulltext.py
+++ b/discovery/fulltext.py
@@ -56,6 +56,21 @@ def fetch_and_save_bibtex(yaml_path):
if not bibtex or "@" not in bibtex:
return None
+ # Normalize month names to the lowercase 3-letter abbreviations that
+ # bibtexparser's `common_strings=True` recognizes. CrossRef sometimes
+ # emits `month=July` (capitalized full name) or `month=Sept` (the
+ # non-standard 4-letter abbreviation), either of which would raise
+ # UndefinedString during parsing.
+ _MONTH_VARIANTS = {
+ "January": "jan", "February": "feb", "March": "mar", "April": "apr",
+ "May": "may", "June": "jun", "July": "jul", "August": "aug",
+ "September": "sep", "October": "oct", "November": "nov",
+ "December": "dec",
+ "Sept": "sep", # non-standard CrossRef abbreviation
+ }
+ for _variant, _abbr in _MONTH_VARIANTS.items():
+ bibtex = re.sub(rf"(month\s*=\s*){_variant}\b", rf"\g<1>{_abbr}", bibtex, flags=re.IGNORECASE)
+
# Save companion .bib file
bib_path = yaml_path.with_suffix(".bib")
bib_path.write_text(bibtex, encoding="utf-8")
diff --git a/pipeline/approved/2024_integration.yaml b/pipeline/approved/2024_integration.yaml
index 320e7c1..589aa4a 100644
--- a/pipeline/approved/2024_integration.yaml
+++ b/pipeline/approved/2024_integration.yaml
@@ -26,8 +26,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Erofeev_2024, title={Integration of Single-Photon Miniature
+ Fluorescence Microscopy and Electrophysiological Recording Methods for in vivo
+ Studying Hippocampal Neuronal Activity}, volume={60}, ISSN={1608-3202}, url={http://dx.doi.org/10.1134/s0022093024040264},
+ DOI={10.1134/s0022093024040264}, number={4}, journal={Journal of Evolutionary Biochemistry
+ and Physiology}, publisher={Pleiades Publishing Ltd}, author={Erofeev, A. I. and
+ Vinokurov, E. K. and Antifeev, I. E. and Vlasova, O. L. and Bezprozvanny, I. B.},
+ year={2024}, month=jul, pages={1586–1606} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/2024_optimizing.yaml b/pipeline/approved/2024_optimizing.yaml
index 2f12f4e..bbe7cf7 100644
--- a/pipeline/approved/2024_optimizing.yaml
+++ b/pipeline/approved/2024_optimizing.yaml
@@ -28,8 +28,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Erofeev_2024, title={On Optimizing Miniscope Data Analysis
+ with Simulated Data: A Study of Parameter Optimization in the Minian Analysis Pipeline},
+ volume={54}, ISSN={1573-899X}, url={http://dx.doi.org/10.1007/s11055-024-01593-y},
+ DOI={10.1007/s11055-024-01593-y}, number={2}, journal={Neuroscience and Behavioral
+ Physiology}, publisher={Springer Science and Business Media LLC}, author={Erofeev,
+ A. I. and Petrushan, M. V. and Lysenko, L. V. and Vinokurov, E. K. and Vlasova,
+ O. L. and Bezprozvanny, I. B.}, year={2024}, month=Feb, pages={251–262} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/aseyev_2024_cadence.yaml b/pipeline/approved/aseyev_2024_cadence.yaml
index 7eeb4e6..7313f50 100644
--- a/pipeline/approved/aseyev_2024_cadence.yaml
+++ b/pipeline/approved/aseyev_2024_cadence.yaml
@@ -29,8 +29,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Aseyev_2024, title={CADENCE — Neuroinformatics Tool for Supervised
+ Calcium Events Detection}, volume={22}, ISSN={1559-0089}, url={http://dx.doi.org/10.1007/s12021-024-09677-3},
+ DOI={10.1007/s12021-024-09677-3}, number={3}, journal={Neuroinformatics}, publisher={Springer
+ Science and Business Media LLC}, author={Aseyev, Nikolay and Borodinova, Anastasia
+ and Pavlova, Svetlana and Roshchina, Marina and Roshchin, Matvey and Nikitin, Evgeny
+ and Balaban, Pavel}, year={2024}, month=jul, pages={379–387} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/barry_2022_dissociable.yaml b/pipeline/approved/barry_2022_dissociable.yaml
index bcabb15..44b88e2 100644
--- a/pipeline/approved/barry_2022_dissociable.yaml
+++ b/pipeline/approved/barry_2022_dissociable.yaml
@@ -34,8 +34,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Barry_2022, title={Dissociable effects of oxycodone on behavior,
+ calcium transient activity, and excitability of dorsolateral striatal neurons},
+ volume={16}, ISSN={1662-5110}, url={http://dx.doi.org/10.3389/fncir.2022.983323},
+ DOI={10.3389/fncir.2022.983323}, journal={Frontiers in Neural Circuits}, publisher={Frontiers
+ Media SA}, author={Barry, Joshua and Oikonomou, Katerina D. and Peng, Allison and
+ Yu, Daniel and Yang, Chenyi and Golshani, Peyman and Evans, Christopher J. and Levine,
+ Michael S. and Cepeda, Carlos}, year={2022}, month=Oct }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/berigan_2023_imaging.yaml b/pipeline/approved/berigan_2023_imaging.yaml
index 1b409dc..591cd4d 100644
--- a/pipeline/approved/berigan_2023_imaging.yaml
+++ b/pipeline/approved/berigan_2023_imaging.yaml
@@ -24,8 +24,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Berigan_2023, title={Imaging neuro-urodynamics of mouse major
+ pelvic ganglion with a micro-endoscopic approach}, volume={129}, ISSN={1522-1598},
+ url={http://dx.doi.org/10.1152/jn.00450.2022}, DOI={10.1152/jn.00450.2022}, number={2},
+ journal={Journal of Neurophysiology}, publisher={American Physiological Society},
+ author={Berigan, Benton R. and Wang, Jing and Schulz, David J. and Ozden, Ilker},
+ year={2023}, month=Feb, pages={479–493} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/borkar_2024_topdown.yaml b/pipeline/approved/borkar_2024_topdown.yaml
index 46bfc5d..d379add 100644
--- a/pipeline/approved/borkar_2024_topdown.yaml
+++ b/pipeline/approved/borkar_2024_topdown.yaml
@@ -45,8 +45,17 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Borkar_2024, title={Top-down control of flight by a non-canonical
+ cortico-amygdala pathway}, volume={625}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-023-06912-w},
+ DOI={10.1038/s41586-023-06912-w}, number={7996}, journal={Nature}, publisher={Springer
+ Science and Business Media LLC}, author={Borkar, Chandrashekhar D. and Stelly, Claire
+ E. and Fu, Xin and Dorofeikova, Maria and Le, Quan-Son Eric and Vutukuri, Rithvik
+ and Vo, Catherine and Walker, Alice Breaux and Basavanhalli, Samhita and Duong,
+ Anh and Bean, Erin and Resendez, Alexis and Parker, Jones G. and Tasker, Jeffrey
+ G. and Fadok, Jonathan P.}, year={2024}, month=Jan, pages={743–749} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/bowles_2021_vagus.yaml b/pipeline/approved/bowles_2021_vagus.yaml
index 67a1768..ffd1edc 100644
--- a/pipeline/approved/bowles_2021_vagus.yaml
+++ b/pipeline/approved/bowles_2021_vagus.yaml
@@ -31,8 +31,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Bowles_2021, title={Vagus nerve stimulation accelerates motor
+ learning through cholinergic modulation}, url={http://dx.doi.org/10.1101/2021.10.28.466306},
+ DOI={10.1101/2021.10.28.466306}, publisher={openRxiv}, author={Bowles, Spencer and
+ Hickman, Jordan and Peng, Xiaoyu and Williamson, W. Ryan and Huang, Rongchen and
+ Washington, Kayden and Donegan, Dane and Welle, Cristin G}, year={2021}, month=Oct
+ }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/bowles_2022_vagus.yaml b/pipeline/approved/bowles_2022_vagus.yaml
index 9b528e1..557c273 100644
--- a/pipeline/approved/bowles_2022_vagus.yaml
+++ b/pipeline/approved/bowles_2022_vagus.yaml
@@ -32,8 +32,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Bowles_2022, title={Vagus nerve stimulation drives selective
+ circuit modulation through cholinergic reinforcement}, volume={110}, ISSN={0896-6273},
+ url={http://dx.doi.org/10.1016/j.neuron.2022.06.017}, DOI={10.1016/j.neuron.2022.06.017},
+ number={17}, journal={Neuron}, publisher={Elsevier BV}, author={Bowles, Spencer
+ and Hickman, Jordan and Peng, Xiaoyu and Williamson, W. Ryan and Huang, Rongchen
+ and Washington, Kayden and Donegan, Dane and Welle, Cristin G.}, year={2022}, month=sep,
+ pages={2867–2885.e7} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/cai_2016_shared.yaml b/pipeline/approved/cai_2016_shared.yaml
index ad47e24..bd74973 100644
--- a/pipeline/approved/cai_2016_shared.yaml
+++ b/pipeline/approved/cai_2016_shared.yaml
@@ -66,7 +66,7 @@ bibtex_raw: ' @article{Cai_2016, title={A shared neural ensemble links distinct
and Veshkini, Michael and La-Vu, Mimi and Lou, Jerry and Flores, Sergio E. and Kim,
Isaac and Sano, Yoshitake and Zhou, Miou and Baumgaertel, Karsten and Lavi, Ayal
and Kamata, Masakazu and Tuszynski, Mark and Mayford, Mark and Golshani, Peyman
- and Silva, Alcino J.}, year={2016}, month=May, pages={115–118} }
+ and Silva, Alcino J.}, year={2016}, month=may, pages={115–118} }
'
bibtex_source: crossref
diff --git a/pipeline/approved/carrasco_2024_monthslong.yaml b/pipeline/approved/carrasco_2024_monthslong.yaml
index 182cde8..9d84c15 100644
--- a/pipeline/approved/carrasco_2024_monthslong.yaml
+++ b/pipeline/approved/carrasco_2024_monthslong.yaml
@@ -21,8 +21,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Carrasco_2024, title={Months-long stability of the head-direction
+ system}, url={http://dx.doi.org/10.1101/2024.06.13.598909}, DOI={10.1101/2024.06.13.598909},
+ publisher={openRxiv}, author={Carrasco, Sofia Skromne and Viejo, Guillaume and Peyrache,
+ Adrien}, year={2024}, month=jun }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/carrasco_2026_monthslong.yaml b/pipeline/approved/carrasco_2026_monthslong.yaml
index bac6255..78c3ae0 100644
--- a/pipeline/approved/carrasco_2026_monthslong.yaml
+++ b/pipeline/approved/carrasco_2026_monthslong.yaml
@@ -21,8 +21,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Skromne_Carrasco_2026, title={Months-long stability of the
+ head-direction system}, volume={652}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-025-10096-w},
+ DOI={10.1038/s41586-025-10096-w}, number={8108}, journal={Nature}, publisher={Springer
+ Science and Business Media LLC}, author={Skromne Carrasco, Sofia and Viejo, Guillaume
+ and Peyrache, Adrien}, year={2026}, month=Feb, pages={167–173} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/chen_2021_fast.yaml b/pipeline/approved/chen_2021_fast.yaml
index 6e35983..f7fc953 100644
--- a/pipeline/approved/chen_2021_fast.yaml
+++ b/pipeline/approved/chen_2021_fast.yaml
@@ -23,8 +23,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @inproceedings{Chen_2021, title={Fast Calcium Trace Extraction for Large-Field-of-View
+ Miniscope}, url={http://dx.doi.org/10.1109/biocas49922.2021.9644936}, DOI={10.1109/biocas49922.2021.9644936},
+ booktitle={2021 IEEE Biomedical Circuits and Systems Conference (BioCAS)}, publisher={IEEE},
+ author={Chen, Zhe and Blair, Garrett J. and Blair, Hugh T. and Cong, Jason}, year={2021},
+ month=Oct, pages={1–5} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/chen_2022_circuit.yaml b/pipeline/approved/chen_2022_circuit.yaml
index bdbaa20..8ad4349 100644
--- a/pipeline/approved/chen_2022_circuit.yaml
+++ b/pipeline/approved/chen_2022_circuit.yaml
@@ -44,8 +44,17 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Chen_2022, title={A circuit from lateral septum neurotensin
+ neurons to tuberal nucleus controls hedonic feeding}, volume={27}, ISSN={1476-5578},
+ url={http://dx.doi.org/10.1038/s41380-022-01742-0}, DOI={10.1038/s41380-022-01742-0},
+ number={12}, journal={Molecular Psychiatry}, publisher={Springer Science and Business
+ Media LLC}, author={Chen, Zijun and Chen, Gaowei and Zhong, Jiafeng and Jiang, Shaolei
+ and Lai, Shishi and Xu, Hua and Deng, Xiaofei and Li, Fengling and Lu, Shanshan
+ and Zhou, Kuikui and Li, Changlin and Liu, Zhongdong and Zhang, Xu and Zhu, Yingjie},
+ year={2022}, month=Aug, pages={4843–4860} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/chen_2022_ubiquitous.yaml b/pipeline/approved/chen_2022_ubiquitous.yaml
index 50c0dc7..c0c595a 100644
--- a/pipeline/approved/chen_2022_ubiquitous.yaml
+++ b/pipeline/approved/chen_2022_ubiquitous.yaml
@@ -28,8 +28,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Chen_2022, title={Ubiquitous proximity to a critical state
+ for collective neural activity in the CA1 region of freely moving mice}, volume={77},
+ ISSN={0577-9073}, url={http://dx.doi.org/10.1016/j.cjph.2021.12.010}, DOI={10.1016/j.cjph.2021.12.010},
+ journal={Chinese Journal of Physics}, publisher={Elsevier BV}, author={Chen, Yi-Ling
+ and Chen, Chun-Chung and Mei, Yu-Ying and Zhou, Ning and Wu, Dongchuan and Lee,
+ Ting-Kuo}, year={2022}, month=jun, pages={497–510} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/chung_2021_cognitive.yaml b/pipeline/approved/chung_2021_cognitive.yaml
index 37e557e..0cfb60b 100644
--- a/pipeline/approved/chung_2021_cognitive.yaml
+++ b/pipeline/approved/chung_2021_cognitive.yaml
@@ -29,8 +29,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Chung_2021, title={Cognitive control persistently enhances
+ hippocampal information processing}, volume={600}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-021-04070-5},
+ DOI={10.1038/s41586-021-04070-5}, number={7889}, journal={Nature}, publisher={Springer
+ Science and Business Media LLC}, author={Chung, Ain and Jou, Claudia and Grau-Perales,
+ Alejandro and Levy, Eliott R. J. and Dvorak, Dino and Hussain, Nida and Fenton,
+ André A.}, year={2021}, month=Nov, pages={484–488} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/dong_2025_simultaneous.yaml b/pipeline/approved/dong_2025_simultaneous.yaml
index 2daaeb1..a2d52ef 100644
--- a/pipeline/approved/dong_2025_simultaneous.yaml
+++ b/pipeline/approved/dong_2025_simultaneous.yaml
@@ -55,7 +55,7 @@ bibtex_raw: ' @article{Dong_2025, title={Simultaneous two-color imaging with a d
Yu and Diego, Keziah and Baggetta, Austin M. and Sweis, Brian M. and Pennington,
Zachary T. and Lamsifer, Sophia I. and Zaki, Yosif and Sangiuliano, Federico and
Philipsberg, Paul A. and Morales-Rodriguez, Denisse and Kircher, Daniel and Slesinger,
- Paul and Shuman, Tristan and Aharoni, Daniel and Cai, Denise J.}, year={2025}, month=July
+ Paul and Shuman, Tristan and Aharoni, Daniel and Cai, Denise J.}, year={2025}, month=jul
}
'
diff --git a/pipeline/approved/etter_2023_optogenetic.yaml b/pipeline/approved/etter_2023_optogenetic.yaml
index a5639fc..ba0020a 100644
--- a/pipeline/approved/etter_2023_optogenetic.yaml
+++ b/pipeline/approved/etter_2023_optogenetic.yaml
@@ -24,8 +24,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Etter_2023, title={Optogenetic frequency scrambling of hippocampal
+ theta oscillations dissociates working memory retrieval from hippocampal spatiotemporal
+ codes}, volume={14}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-023-35825-5},
+ DOI={10.1038/s41467-023-35825-5}, number={1}, journal={Nature Communications}, publisher={Springer
+ Science and Business Media LLC}, author={Etter, Guillaume and van der Veldt, Suzanne
+ and Choi, Jisoo and Williams, Sylvain}, year={2023}, month=Jan }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/farrell_2021_midbrain.yaml b/pipeline/approved/farrell_2021_midbrain.yaml
index c991ca2..385fd8c 100644
--- a/pipeline/approved/farrell_2021_midbrain.yaml
+++ b/pipeline/approved/farrell_2021_midbrain.yaml
@@ -21,8 +21,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Farrell_2021, title={Midbrain dopamine neurons provide teaching
+ signals for goal-directed navigation}, url={http://dx.doi.org/10.1101/2021.02.17.431585},
+ DOI={10.1101/2021.02.17.431585}, publisher={openRxiv}, author={Farrell, Karolina
+ and Lak, Armin and Saleem, Aman B}, year={2021}, month=Feb }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/gabriel_2022_behaviordepot.yaml b/pipeline/approved/gabriel_2022_behaviordepot.yaml
index 5b68854..24d6e68 100644
--- a/pipeline/approved/gabriel_2022_behaviordepot.yaml
+++ b/pipeline/approved/gabriel_2022_behaviordepot.yaml
@@ -44,8 +44,17 @@ source: openalex_cites
seed_paper_doi: 10.1038/s41593-019-0559-0
discovered_date: '2026-04-10'
batch_id: backlog_2026-04-10
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Gabriel_2022, title={BehaviorDEPOT is a simple, flexible tool
+ for automated behavioral detection based on markerless pose tracking}, volume={11},
+ ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.74314}, DOI={10.7554/elife.74314},
+ journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Gabriel,
+ Christopher J and Zeidler, Zachary and Jin, Benita and Guo, Changliang and Goodpaster,
+ Caitlin M and Kashay, Adrienne Q and Wu, Anna and Delaney, Molly and Cheung, Jovian
+ and DiFazio, Lauren E and Sharpe, Melissa J and Aharoni, Daniel and Wilke, Scott
+ A and DeNardo, Laura A}, year={2022}, month=Aug }
+
+ '
+bibtex_source: crossref
fulltext:
source: unpaywall
pdf_local_path: null
diff --git a/pipeline/approved/gagliardi_2024_distinct.yaml b/pipeline/approved/gagliardi_2024_distinct.yaml
index 9e039e8..71d73a9 100644
--- a/pipeline/approved/gagliardi_2024_distinct.yaml
+++ b/pipeline/approved/gagliardi_2024_distinct.yaml
@@ -38,7 +38,7 @@ bibtex_raw: ' @article{Gagliardi_2024, title={Distinct neural mechanisms for hea
DOI={10.1038/s41467-024-50112-7}, number={1}, journal={Nature Communications}, publisher={Springer
Science and Business Media LLC}, author={Gagliardi, Celia M. and Normandin, Marc
E. and Keinath, Alexandra T. and Julian, Joshua B. and Lopez, Matthew R. and Ramos-Alvarez,
- Manuel-Miguel and Epstein, Russell A. and Muzzio, Isabel A.}, year={2024}, month=July
+ Manuel-Miguel and Epstein, Russell A. and Muzzio, Isabel A.}, year={2024}, month=jul
}
'
diff --git a/pipeline/approved/gao_2020_novel.yaml b/pipeline/approved/gao_2020_novel.yaml
index 0afb063..7a48b2e 100644
--- a/pipeline/approved/gao_2020_novel.yaml
+++ b/pipeline/approved/gao_2020_novel.yaml
@@ -27,8 +27,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @inproceedings{Gao_2020, title={Novel Virtual Reality System for Auditory
+ Tasks in Head-fixed Mice}, url={http://dx.doi.org/10.1109/embc44109.2020.9176536},
+ DOI={10.1109/embc44109.2020.9176536}, booktitle={2020 42nd Annual International
+ Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)}, publisher={IEEE},
+ author={Gao, Sibo and Webb, James and Mridha, Zakir and Banta, Anton and Kemere,
+ Caleb and McGinley, Matthew}, year={2020}, month=jul, pages={2925–2928} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/hart_2020_chemogenetic.yaml b/pipeline/approved/hart_2020_chemogenetic.yaml
index 91b0fe2..2aef1d8 100644
--- a/pipeline/approved/hart_2020_chemogenetic.yaml
+++ b/pipeline/approved/hart_2020_chemogenetic.yaml
@@ -26,8 +26,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Hart_2020, title={Chemogenetic Modulation and Single-Photon
+ Calcium Imaging in Anterior Cingulate Cortex Reveal a Mechanism for Effort-Based
+ Decisions}, volume={40}, ISSN={1529-2401}, url={http://dx.doi.org/10.1523/jneurosci.2548-19.2020},
+ DOI={10.1523/jneurosci.2548-19.2020}, number={29}, journal={The Journal of Neuroscience},
+ publisher={Society for Neuroscience}, author={Hart, Evan E. and Blair, Garrett J.
+ and O’Dell, Thomas J. and Blair, Hugh T. and Izquierdo, Alicia}, year={2020}, month=jun,
+ pages={5628–5643} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/hayashi_2021_largescale.yaml b/pipeline/approved/hayashi_2021_largescale.yaml
index 25e2734..abef350 100644
--- a/pipeline/approved/hayashi_2021_largescale.yaml
+++ b/pipeline/approved/hayashi_2021_largescale.yaml
@@ -22,8 +22,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Hayashi_2021, title={Large-scale calcium imaging with a head-mounted
+ axial scanning 3D fluorescence microscope}, url={http://dx.doi.org/10.1101/2021.01.20.427512},
+ DOI={10.1101/2021.01.20.427512}, publisher={openRxiv}, author={Hayashi, Yuichiro
+ and Kobayakawa, Ko and Kobayakawa, Reiko}, year={2021}, month=Jan }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/hirano_2022_impact.yaml b/pipeline/approved/hirano_2022_impact.yaml
index e14c319..f8b40f4 100644
--- a/pipeline/approved/hirano_2022_impact.yaml
+++ b/pipeline/approved/hirano_2022_impact.yaml
@@ -24,8 +24,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Hirano_2022, title={The impact of pitolisant, an H3 receptor
+ antagonist/inverse agonist, on perirhinal cortex activity in individual neuron and
+ neuronal population levels}, volume={12}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-022-11032-y},
+ DOI={10.1038/s41598-022-11032-y}, number={1}, journal={Scientific Reports}, publisher={Springer
+ Science and Business Media LLC}, author={Hirano, Kyosuke and Morishita, Yoshikazu
+ and Minami, Masabumi and Nomura, Hiroshi}, year={2022}, month=may }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/hsiao_2021_using.yaml b/pipeline/approved/hsiao_2021_using.yaml
index a01cf97..9d6f689 100644
--- a/pipeline/approved/hsiao_2021_using.yaml
+++ b/pipeline/approved/hsiao_2021_using.yaml
@@ -24,8 +24,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Hsiao_2021, title={Using Baseplating and a Miniscope Preanchored
+ with an Objective Lens for Calcium Transient Research in Mice}, ISSN={1940-087X},
+ url={http://dx.doi.org/10.3791/62611}, DOI={10.3791/62611}, number={172}, journal={Journal
+ of Visualized Experiments}, publisher={MyJove Corporation}, author={Hsiao, Yi-Tse
+ and Wang, Angela Yu-Chi and Lee, Ting-Yen and Chang, Ching-Yuan}, year={2021}, month=jun
+ }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/jameson_2023_vagal.yaml b/pipeline/approved/jameson_2023_vagal.yaml
index 781c5ab..0261b43 100644
--- a/pipeline/approved/jameson_2023_vagal.yaml
+++ b/pipeline/approved/jameson_2023_vagal.yaml
@@ -37,8 +37,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Jameson_2023, title={Vagal interoception of microbial metabolites
+ from the small intestinal lumen}, url={http://dx.doi.org/10.1101/2023.12.18.572257},
+ DOI={10.1101/2023.12.18.572257}, publisher={openRxiv}, author={Jameson, Kelly G.
+ and Kazmi, Sabeen A. and Son, Celine and Mazdeyasnan, Donya and Leshan, Emma and
+ Vuong, Helen E. and Paramo, Jorge and Lopez-Romero, Arlene and Yang, Long and Schweizer,
+ Felix E. and Hsiao, Elaine Y.}, year={2023}, month=Dec }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/jendryka_2024_excitatory.yaml b/pipeline/approved/jendryka_2024_excitatory.yaml
index f67ef1a..f10bb36 100644
--- a/pipeline/approved/jendryka_2024_excitatory.yaml
+++ b/pipeline/approved/jendryka_2024_excitatory.yaml
@@ -36,8 +36,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Jendryka_2024, title={Excitatory neurons of the anterior cingulate
+ cortex encode chosen actions and their outcomes rather than cognitive state}, url={http://dx.doi.org/10.1101/2024.04.12.589244},
+ DOI={10.1101/2024.04.12.589244}, publisher={openRxiv}, author={Jendryka, Martin
+ M. and Lewin, Uwe and Kapanaiah, Sampath K.T. and Dermutz, Hartmut and Liss, Birgit
+ and Pekcec, Anton and Akam, Thomas and Grewe, Benjamin F. and Kätzel, Dennis}, year={2024},
+ month=Apr }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/johnson_2022_highly.yaml b/pipeline/approved/johnson_2022_highly.yaml
index 346124d..2c37aac 100644
--- a/pipeline/approved/johnson_2022_highly.yaml
+++ b/pipeline/approved/johnson_2022_highly.yaml
@@ -58,8 +58,20 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Johnson_2022, title={Highly unstable heterogeneous representations
+ in VIP interneurons of the anterior cingulate cortex}, volume={27}, ISSN={1476-5578},
+ url={http://dx.doi.org/10.1038/s41380-022-01485-y}, DOI={10.1038/s41380-022-01485-y},
+ number={5}, journal={Molecular Psychiatry}, publisher={Springer Science and Business
+ Media LLC}, author={Johnson, Connor and Kretsge, Lisa N. and Yen, William W. and
+ Sriram, Balaji and O’Connor, Alexandra and Liu, Ruichen Sky and Jimenez, Jessica
+ C. and Phadke, Rhushikesh A. and Wingfield, Kelly K. and Yeung, Charlotte and Jinadasa,
+ Tushare J. and Nguyen, Thanh P. H. and Cho, Eun Seon and Fuchs, Erelle and Spevack,
+ Eli D. and Velasco, Berta Escude and Hausmann, Frances S. and Fournier, Luke A.
+ and Brack, Alison and Melzer, Sarah and Cruz-Martín, Alberto}, year={2022}, month=Mar,
+ pages={2602–2618} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/juneau_2018_enhanced.yaml b/pipeline/approved/juneau_2018_enhanced.yaml
index d0e63bd..bd512e3 100644
--- a/pipeline/approved/juneau_2018_enhanced.yaml
+++ b/pipeline/approved/juneau_2018_enhanced.yaml
@@ -23,8 +23,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @inproceedings{Juneau_2018, title={Enhanced Image Sensor Module for
+ Head-Mounted Microscopes}, url={http://dx.doi.org/10.1109/embc.2018.8512387}, DOI={10.1109/embc.2018.8512387},
+ booktitle={2018 40th Annual International Conference of the IEEE Engineering in
+ Medicine and Biology Society (EMBC)}, publisher={IEEE}, author={Juneau, Jill and
+ Duret, Guillaume and Robinson, Jacob and Kemere, Caleb}, year={2018}, month=jul,
+ pages={826–829} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/kapanaiah_2023_openmac.yaml b/pipeline/approved/kapanaiah_2023_openmac.yaml
index b25266f..3391417 100644
--- a/pipeline/approved/kapanaiah_2023_openmac.yaml
+++ b/pipeline/approved/kapanaiah_2023_openmac.yaml
@@ -20,8 +20,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Kapanaiah_2023, title={Open-MAC: A low-cost open-source motorized
+ commutator for electro- and opto-physiological recordings in freely moving rodents},
+ volume={14}, ISSN={2468-0672}, url={http://dx.doi.org/10.1016/j.ohx.2023.e00429},
+ DOI={10.1016/j.ohx.2023.e00429}, journal={HardwareX}, publisher={Elsevier BV}, author={Kapanaiah,
+ Sampath K.T. and Kätzel, Dennis}, year={2023}, month=jun, pages={e00429} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/keinath_2022_representation.yaml b/pipeline/approved/keinath_2022_representation.yaml
index 9278361..e50e7ce 100644
--- a/pipeline/approved/keinath_2022_representation.yaml
+++ b/pipeline/approved/keinath_2022_representation.yaml
@@ -22,8 +22,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Keinath_2022, title={The representation of context in mouse
+ hippocampus is preserved despite neural drift}, volume={13}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-022-30198-7},
+ DOI={10.1038/s41467-022-30198-7}, number={1}, journal={Nature Communications}, publisher={Springer
+ Science and Business Media LLC}, author={Keinath, Alexandra T. and Mosser, Coralie-Anne
+ and Brandon, Mark P.}, year={2022}, month=may }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/kingsbury_2019_correlated.yaml b/pipeline/approved/kingsbury_2019_correlated.yaml
index f13c759..e6deecb 100644
--- a/pipeline/approved/kingsbury_2019_correlated.yaml
+++ b/pipeline/approved/kingsbury_2019_correlated.yaml
@@ -30,8 +30,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Kingsbury_2019, title={Correlated Neural Activity and Encoding
+ of Behavior across Brains of Socially Interacting Animals}, volume={178}, ISSN={0092-8674},
+ url={http://dx.doi.org/10.1016/j.cell.2019.05.022}, DOI={10.1016/j.cell.2019.05.022},
+ number={2}, journal={Cell}, publisher={Elsevier BV}, author={Kingsbury, Lyle and
+ Huang, Shan and Wang, Jun and Gu, Ken and Golshani, Peyman and Wu, Ye Emily and
+ Hong, Weizhe}, year={2019}, month=jul, pages={429–446.e16} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/kingsbury_2020_cortical.yaml b/pipeline/approved/kingsbury_2020_cortical.yaml
index 4e72d87..05e2933 100644
--- a/pipeline/approved/kingsbury_2020_cortical.yaml
+++ b/pipeline/approved/kingsbury_2020_cortical.yaml
@@ -31,8 +31,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Kingsbury_2020, title={Cortical Representations of Conspecific
+ Sex Shape Social Behavior}, volume={107}, ISSN={0896-6273}, url={http://dx.doi.org/10.1016/j.neuron.2020.06.020},
+ DOI={10.1016/j.neuron.2020.06.020}, number={5}, journal={Neuron}, publisher={Elsevier
+ BV}, author={Kingsbury, Lyle and Huang, Shan and Raam, Tara and Ye, Letizia S. and
+ Wei, Don and Hu, Rongfeng K. and Ye, Li and Hong, Weizhe}, year={2020}, month=sep,
+ pages={941–953.e7} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/larosa_2024_social.yaml b/pipeline/approved/larosa_2024_social.yaml
index 2039572..bebc348 100644
--- a/pipeline/approved/larosa_2024_social.yaml
+++ b/pipeline/approved/larosa_2024_social.yaml
@@ -27,8 +27,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Larosa_2024, title={Social valence dictates sex differences
+ in identity recognition}, url={http://dx.doi.org/10.1101/2024.06.07.598039}, DOI={10.1101/2024.06.07.598039},
+ publisher={openRxiv}, author={Larosa, Amanda and Xu, Qi Wei and Wong, Alice S. and
+ Lee, J. Quinn and Brandon, Mark P. and Wong, Tak Pan}, year={2024}, month=jun }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/lee_2023_identifying.yaml b/pipeline/approved/lee_2023_identifying.yaml
index a6684e5..307330b 100644
--- a/pipeline/approved/lee_2023_identifying.yaml
+++ b/pipeline/approved/lee_2023_identifying.yaml
@@ -24,8 +24,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Lee_2023, title={Identifying representational structure in
+ CA1 to benchmark theoretical models of cognitive mapping}, url={http://dx.doi.org/10.1101/2023.10.08.561112},
+ DOI={10.1101/2023.10.08.561112}, publisher={openRxiv}, author={Lee, J. Quinn and
+ Keinath, Alexandra T. and Cianfarano, Erica and Brandon, Mark P.}, year={2023},
+ month=Oct }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/li_2024_cholecystokinin.yaml b/pipeline/approved/li_2024_cholecystokinin.yaml
index 370d98f..6a16471 100644
--- a/pipeline/approved/li_2024_cholecystokinin.yaml
+++ b/pipeline/approved/li_2024_cholecystokinin.yaml
@@ -34,8 +34,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Li_2024, title={Cholecystokinin facilitates motor skill learning
+ by modulating neuroplasticity in the motor cortex}, volume={13}, ISSN={2050-084X},
+ url={http://dx.doi.org/10.7554/elife.83897}, DOI={10.7554/elife.83897}, journal={eLife},
+ publisher={eLife Sciences Publications, Ltd}, author={Li, Hao and Feng, Jingyu and
+ Chen, Mengying and Xin, Min and Chen, Xi and Liu, Wenhao and Wang, Liping and Wang,
+ Kuan Hong and He, Jufang}, year={2024}, month=may }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/li_2024_stable.yaml b/pipeline/approved/li_2024_stable.yaml
index f77b130..1da7591 100644
--- a/pipeline/approved/li_2024_stable.yaml
+++ b/pipeline/approved/li_2024_stable.yaml
@@ -32,8 +32,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Li_2024, title={Stable sequential dynamics in prefrontal cortex
+ represents subjective estimation of time}, url={http://dx.doi.org/10.1101/2024.02.26.582071},
+ DOI={10.1101/2024.02.26.582071}, publisher={openRxiv}, author={Li, Yiting and Yin,
+ Wenqu and Wang, Xin and Li, Jiawen and Zhou, Shanglin and Ma, Chaolin and Yuan,
+ Peng and Li, Baoming}, year={2024}, month=Feb }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/lin_2024_hippocampal.yaml b/pipeline/approved/lin_2024_hippocampal.yaml
index 7689a4c..40f6733 100644
--- a/pipeline/approved/lin_2024_hippocampal.yaml
+++ b/pipeline/approved/lin_2024_hippocampal.yaml
@@ -20,8 +20,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Lin_2024, title={Hippocampal and orbitofrontal neurons contribute
+ to complementary aspects of associative structure}, volume={15}, ISSN={2041-1723},
+ url={http://dx.doi.org/10.1038/s41467-024-49652-9}, DOI={10.1038/s41467-024-49652-9},
+ number={1}, journal={Nature Communications}, publisher={Springer Science and Business
+ Media LLC}, author={Lin, Huixin and Zhou, Jingfeng}, year={2024}, month=jun }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/long_2024_constraints.yaml b/pipeline/approved/long_2024_constraints.yaml
index ae8add6..aa705c7 100644
--- a/pipeline/approved/long_2024_constraints.yaml
+++ b/pipeline/approved/long_2024_constraints.yaml
@@ -28,8 +28,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Long_2024, title={Constraints on the subsecond modulation of
+ striatal dynamics by physiological dopamine signaling}, volume={27}, ISSN={1546-1726},
+ url={http://dx.doi.org/10.1038/s41593-024-01699-z}, DOI={10.1038/s41593-024-01699-z},
+ number={10}, journal={Nature Neuroscience}, publisher={Springer Science and Business
+ Media LLC}, author={Long, Charltien and Lee, Kwang and Yang, Long and Dafalias,
+ Theresia and Wu, Alexander K. and Masmanidis, Sotiris C.}, year={2024}, month=jul,
+ pages={1977–1986} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/mishchanchuk_2024_hidden.yaml b/pipeline/approved/mishchanchuk_2024_hidden.yaml
index 0ac472a..77dac06 100644
--- a/pipeline/approved/mishchanchuk_2024_hidden.yaml
+++ b/pipeline/approved/mishchanchuk_2024_hidden.yaml
@@ -30,8 +30,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Mishchanchuk_2024, title={Hidden state inference requires abstract
+ contextual representations in ventral hippocampus}, url={http://dx.doi.org/10.1101/2024.05.17.594673},
+ DOI={10.1101/2024.05.17.594673}, publisher={openRxiv}, author={Mishchanchuk, Karyna
+ and Gregoriou, Gabrielle and Qü, Albert and Kastler, Alizée and Huys, Quentin and
+ Wilbrecht, Linda and MacAskill, Andrew F.}, year={2024}, month=may }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/nogueira_2020_loud.yaml b/pipeline/approved/nogueira_2020_loud.yaml
index 48ba977..530fb41 100644
--- a/pipeline/approved/nogueira_2020_loud.yaml
+++ b/pipeline/approved/nogueira_2020_loud.yaml
@@ -28,8 +28,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Nogueira_2020, title={Loud noise exposure differentially affects
+ subpopulations of auditory cortex pyramidal cells}, url={http://dx.doi.org/10.1101/2020.08.25.264200},
+ DOI={10.1101/2020.08.25.264200}, publisher={openRxiv}, author={Nogueira, Ingrid
+ and Winne, Jessica and Lima, Thiago Z. and Malfatti, Thawann and Leao, Richardson
+ N. and Leao, Katarina E.}, year={2020}, month=Aug }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/petter_2023_elucidating.yaml b/pipeline/approved/petter_2023_elucidating.yaml
index b230932..9fd154e 100644
--- a/pipeline/approved/petter_2023_elucidating.yaml
+++ b/pipeline/approved/petter_2023_elucidating.yaml
@@ -29,8 +29,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Petter_2023, title={Elucidating a locus coeruleus-dentate gyrus
+ dopamine pathway for operant reinforcement}, volume={12}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.83600},
+ DOI={10.7554/elife.83600}, journal={eLife}, publisher={eLife Sciences Publications,
+ Ltd}, author={Petter, Elijah A and Fallon, Isabella P and Hughes, Ryan N and Watson,
+ Glenn DR and Meck, Warren H and Ulloa Severino, Francesco Paolo and Yin, Henry H},
+ year={2023}, month=Apr }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/rozeske_2023_representational.yaml b/pipeline/approved/rozeske_2023_representational.yaml
index fa5c146..8c4da30 100644
--- a/pipeline/approved/rozeske_2023_representational.yaml
+++ b/pipeline/approved/rozeske_2023_representational.yaml
@@ -26,8 +26,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Rozeske_2023, title={Representational similarity supports rapid
+ context retrieval during fear discrimination in ventral hippocampus}, url={http://dx.doi.org/10.1101/2023.09.08.556889},
+ DOI={10.1101/2023.09.08.556889}, publisher={openRxiv}, author={Rozeske, Robert R.
+ and Runtz, Léonie and Keinath, Alexandra T. and Sossin, Aaron and Brandon, Mark
+ P.}, year={2023}, month=sep }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/simone_2018_role.yaml b/pipeline/approved/simone_2018_role.yaml
index 78cf47f..32c0535 100644
--- a/pipeline/approved/simone_2018_role.yaml
+++ b/pipeline/approved/simone_2018_role.yaml
@@ -18,8 +18,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: "@article{https://doi.org/10.11588/heidok.00025508,\n doi = {10.11588/HEIDOK.00025508},\n\
+ \ url = {http://archiv.ub.uni-heidelberg.de/volltextserver/id/eprint/25508},\n\
+ \ author = {Pfarr, Simone},\n keywords = {570 Life sciences},\n title = {The\
+ \ Role of the Medial Prefrontal Cortex in Reward Seeking: Functional Evidence on\
+ \ Cellular and Molecular Mechanisms underlying Drug and Natural Reward Seeking},\n\
+ \ publisher = {Heidelberg University Library},\n year = {2018}\n}\n"
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/souza_2024_miniscope.yaml b/pipeline/approved/souza_2024_miniscope.yaml
index d00febf..f002aad 100644
--- a/pipeline/approved/souza_2024_miniscope.yaml
+++ b/pipeline/approved/souza_2024_miniscope.yaml
@@ -36,8 +36,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Simoes_de_Souza_2024, title={Miniscope Recording Calcium Signals
+ at Hippocampus of Mice Navigating an Odor Plume}, url={http://dx.doi.org/10.1101/2024.06.12.598681},
+ DOI={10.1101/2024.06.12.598681}, publisher={openRxiv}, author={Simoes de Souza,
+ Fabio M. and Williamson, Ryan and McCullough, Connor and Teel, Alec and Futia, Gregory
+ and Ma, Ming and True, Aaron and Crimaldi, John. P. and Gibson, Emily and Restrepo,
+ Diego}, year={2024}, month=jun }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/vu_2024_targeted.yaml b/pipeline/approved/vu_2024_targeted.yaml
index bd4d6c1..ed06b3c 100644
--- a/pipeline/approved/vu_2024_targeted.yaml
+++ b/pipeline/approved/vu_2024_targeted.yaml
@@ -48,8 +48,18 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Vu_2024, title={Targeted micro-fiber arrays for measuring and
+ manipulating localized multi-scale neural dynamics over large, deep brain volumes
+ during behavior}, volume={112}, ISSN={0896-6273}, url={http://dx.doi.org/10.1016/j.neuron.2023.12.011},
+ DOI={10.1016/j.neuron.2023.12.011}, number={6}, journal={Neuron}, publisher={Elsevier
+ BV}, author={Vu, Mai-Anh T. and Brown, Eleanor H. and Wen, Michelle J. and Noggle,
+ Christian A. and Zhang, Zicheng and Monk, Kevin J. and Bouabid, Safa and Mroz, Lydia
+ and Graham, Benjamin M. and Zhuo, Yizhou and Li, Yulong and Otchy, Timothy M. and
+ Tian, Lin and Davison, Ian G. and Boas, David A. and Howe, Mark W.}, year={2024},
+ month=Mar, pages={909–923.e9} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/wang_2023_somatic.yaml b/pipeline/approved/wang_2023_somatic.yaml
index 4f712e5..84953d2 100644
--- a/pipeline/approved/wang_2023_somatic.yaml
+++ b/pipeline/approved/wang_2023_somatic.yaml
@@ -26,8 +26,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Wang_2023, title={Somatic Calcium Signals from Layer II/III
+ Motor Cortex for Continuous Neural Decoding}, url={http://dx.doi.org/10.1101/2023.04.11.536319},
+ DOI={10.1101/2023.04.11.536319}, publisher={openRxiv}, author={Wang, Ruixue and
+ Han, Jiawei and Hu, Xiaoling and You, Heecheon and Zhang, Shaomin}, year={2023},
+ month=Apr }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/wang_2024_tscope.yaml b/pipeline/approved/wang_2024_tscope.yaml
index fc0535c..3d7eea2 100644
--- a/pipeline/approved/wang_2024_tscope.yaml
+++ b/pipeline/approved/wang_2024_tscope.yaml
@@ -36,8 +36,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Wang_2024, title={T-scope V4: miniaturized microscope for optogenetic
+ tagging in freely behaving animals}, url={http://dx.doi.org/10.1101/2024.10.07.616920},
+ DOI={10.1101/2024.10.07.616920}, publisher={openRxiv}, author={Wang, Yuteng and
+ Vergara, Pablo and Hasegawa, Satoshi and Tomita, Naoki and Cherasse, Yoan and Naoi,
+ Toshie and Sakurai, Takeshi and Sugaya, Yuki and Kano, Masanobu and Sakaguchi, Masanori},
+ year={2024}, month=Oct }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/wu_2021_neural.yaml b/pipeline/approved/wu_2021_neural.yaml
index 2222157..e683a9d 100644
--- a/pipeline/approved/wu_2021_neural.yaml
+++ b/pipeline/approved/wu_2021_neural.yaml
@@ -29,8 +29,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Wu_2021, title={Neural control of affiliative touch in prosocial
+ interaction}, volume={599}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-021-03962-w},
+ DOI={10.1038/s41586-021-03962-w}, number={7884}, journal={Nature}, publisher={Springer
+ Science and Business Media LLC}, author={Wu, Ye Emily and Dang, James and Kingsbury,
+ Lyle and Zhang, Mingmin and Sun, Fangmiao and Hu, Rongfeng K. and Hong, Weizhe},
+ year={2021}, month=Oct, pages={262–267} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/yan_2018_implementing.yaml b/pipeline/approved/yan_2018_implementing.yaml
index 22013ef..7e29a87 100644
--- a/pipeline/approved/yan_2018_implementing.yaml
+++ b/pipeline/approved/yan_2018_implementing.yaml
@@ -5,7 +5,7 @@ pmcid: null
title: Implementing simultaneous calcium imaging and optogenetics in freely moving
rodents to investigate the role of local inhibition in place field stability
authors:
-- first: Helena
+- first: Helena Z. H.
last: Yan
journal: Wellesley College Digital RepositoryWellesley (Wellesley College)
publication_year: 2018
@@ -18,8 +18,12 @@ source: openalex_cites
seed_paper_doi: 10.1038/nature17955
discovered_date: '2026-04-10'
batch_id: backlog_2026-04-10
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: "@mastersthesis{yan_2018_implementing,\n title = {Implementing simultaneous\
+ \ calcium imaging and optogenetics in freely moving rodents to investigate the role\
+ \ of local inhibition in place field stability},\n author = {Yan, Helena Z. H.},\n\
+ \ school = {Wellesley College},\n year = {2018},\n month = may,\n url \
+ \ = {https://repository.wellesley.edu/thesiscollection/574},\n}\n"
+bibtex_source: trusted_bib_manual
fulltext:
source: null
pdf_local_path: null
@@ -29,11 +33,21 @@ analysis:
confidence: null
tools_identified: []
evidence: []
- paper_type: null
+ paper_type: Methods
suggested_component: null
suggested_technique: null
- reasoning: null
- suggested_project: Miniscope DAQ
+ reasoning: Wellesley College senior thesis (no DOI assigned by repo). BibTeX hand-crafted
+ from trusted-bib metadata + Wellesley repository URL. Author list reduced to Helena
+ Yan (candidate); Wilson/Newman/Wasserman/Wiest were committee in the trusted bib
+ but aren't BibTeX co-authors. paper_type=Methods (thesis implements simultaneous
+ imaging+opto rig); project=V3+DAQ per trusted-bib tags.
+ suggested_project: Miniscope V3, Miniscope DAQ
+ suggested_keywords:
+ - Calcium Imaging
+ - Optogenetics
+ - Place Cells
+ - Hippocampus
+ - Open-Source
stage: approved
stage_history:
- stage: candidate
diff --git a/pipeline/approved/yanny_2020_miniscope3d.yaml b/pipeline/approved/yanny_2020_miniscope3d.yaml
index fd9ba30..ae82083 100644
--- a/pipeline/approved/yanny_2020_miniscope3d.yaml
+++ b/pipeline/approved/yanny_2020_miniscope3d.yaml
@@ -33,8 +33,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Yanny_2020, title={Miniscope3D: optimized single-shot miniature
+ 3D fluorescence microscopy}, volume={9}, ISSN={2047-7538}, url={http://dx.doi.org/10.1038/s41377-020-00403-7},
+ DOI={10.1038/s41377-020-00403-7}, number={1}, journal={Light: Science & Applications},
+ publisher={Springer Science and Business Media LLC}, author={Yanny, Kyrollos and
+ Antipa, Nick and Liberti, William and Dehaeck, Sam and Monakhova, Kristina and Liu,
+ Fanglin Linda and Shen, Konlin and Ng, Ren and Waller, Laura}, year={2020}, month=Oct
+ }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/zhang_2023_novel.yaml b/pipeline/approved/zhang_2023_novel.yaml
index c80b752..17df122 100644
--- a/pipeline/approved/zhang_2023_novel.yaml
+++ b/pipeline/approved/zhang_2023_novel.yaml
@@ -19,8 +19,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Zhang_2023, title={A Novel Design Method of Uniformity Energy
+ Distribution Lens for Miniscopes}, volume={15}, ISSN={1943-0647}, url={http://dx.doi.org/10.1109/jphot.2023.3306806},
+ DOI={10.1109/jphot.2023.3306806}, number={5}, journal={IEEE Photonics Journal},
+ publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Zhang,
+ Jinyong and Xin, Xuegang}, year={2023}, month=Oct, pages={1–6} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/pipeline/approved/zhang_2024_cortical.yaml b/pipeline/approved/zhang_2024_cortical.yaml
index 2ca6912..35f056a 100644
--- a/pipeline/approved/zhang_2024_cortical.yaml
+++ b/pipeline/approved/zhang_2024_cortical.yaml
@@ -23,8 +23,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
-bibtex_raw: null
-bibtex_source: null
+bibtex_raw: ' @article{Zhang_2024, title={Cortical regulation of helping behaviour
+ towards others in pain}, volume={626}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-023-06973-x},
+ DOI={10.1038/s41586-023-06973-x}, number={7997}, journal={Nature}, publisher={Springer
+ Science and Business Media LLC}, author={Zhang, Mingmin and Wu, Ye Emily and Jiang,
+ Mengping and Hong, Weizhe}, year={2024}, month=Jan, pages={136–144} }
+
+ '
+bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
diff --git a/references.bib b/references.bib
index 88f5104..fc0bfcd 100644
--- a/references.bib
+++ b/references.bib
@@ -228,3 +228,2428 @@ @article{madruga_2025_opensource
volume = {16},
year = {2025}
}
+
+@article{berndt_2023_current,
+ author = {Berndt, Andre and Cai, Denise and Cohen, Adam and Juarez, Barbara and Iglesias, Jaume Taura and Xiong, Hejian and Qin, Zhenpeng and Tian, Lin and Slesinger, Paul A.},
+ doi = {10.1523/jneurosci.1391-23.2023},
+ issn = {1529-2401},
+ journal = {The Journal of Neuroscience},
+ month = {November},
+ number = {45},
+ pages = {7587–7598},
+ paper_type = {Review},
+ project = {Miniscope V4},
+ publisher = {Society for Neuroscience},
+ title = {Current Status and Future Strategies for Advancing Functional Circuit MappingIn Vivo},
+ url = {http://dx.doi.org/10.1523/jneurosci.1391-23.2023},
+ volume = {43},
+ year = {2023}
+}
+
+@article{blair_2023_hippocampal,
+ author = {Blair, Garrett J and Guo, Changliang and Wang, Shiyun and Fanselow, Michael S and Golshani, Peyman and Aharoni, Daniel and Blair, Hugh T},
+ doi = {10.7554/elife.80661},
+ issn = {2050-084X},
+ journal = {eLife},
+ keywords = {Calcium Imaging, Hippocampus, Memory, Place Cells},
+ month = {July},
+ paper_type = {Science},
+ project = {MiniLFOV},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {Hippocampal place cell remapping occurs with memory storage of aversive experiences},
+ url = {http://dx.doi.org/10.7554/elife.80661},
+ volume = {12},
+ year = {2023}
+}
+
+@article{van_den_boom_2023_unraveling,
+ author = {van den Boom, Bastijn J. G. and Elhazaz-Fernandez, Alfredo and Rasmussen, Peter A. and van Beest, Enny H. and Parthasarathy, Aishwarya and Denys, Damiaan and Willuhn, Ingo},
+ doi = {10.1038/s41467-023-41026-x},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ month = {September},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Unraveling the mechanisms of deep-brain stimulation of the internal capsule in a mouse model},
+ url = {http://dx.doi.org/10.1038/s41467-023-41026-x},
+ volume = {14},
+ year = {2023}
+}
+
+@article{cai_2016_shared,
+ author = {Cai, Denise J. and Aharoni, Daniel and Shuman, Tristan and Shobe, Justin and Biane, Jeremy and Song, Weilin and Wei, Brandon and Veshkini, Michael and La-Vu, Mimi and Lou, Jerry and Flores, Sergio E. and Kim, Isaac and Sano, Yoshitake and Zhou, Miou and Baumgaertel, Karsten and Lavi, Ayal and Kamata, Masakazu and Tuszynski, Mark and Mayford, Mark and Golshani, Peyman and Silva, Alcino J.},
+ doi = {10.1038/nature17955},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Memory, Hippocampus},
+ month = {May},
+ number = {7605},
+ pages = {115–118},
+ paper_type = {Tool Paper},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {A shared neural ensemble links distinct contextual memories encoded close in time},
+ url = {http://dx.doi.org/10.1038/nature17955},
+ volume = {534},
+ year = {2016}
+}
+
+@inproceedings{celinskis_2020_miniaturized,
+ author = {Celinskis, Dmitrijs and Friedman, Nina and Koksharov, Mikhail and Murphy, Jeremy and Gomez-Ramirez, Manuel and Borton, David and Shaner, Nathan and Hochgeschwender, Ute and Lipscombe, Diane and Moore, Christopher},
+ booktitle = {2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)},
+ doi = {10.1109/embc44109.2020.9175375},
+ month = {July},
+ pages = {4385–4389},
+ project = {Miniscope V3},
+ publisher = {IEEE},
+ title = {Miniaturized Devices for Bioluminescence Imaging in Freely Behaving Animals},
+ url = {http://dx.doi.org/10.1109/embc44109.2020.9175375},
+ year = {2020}
+}
+
+@article{celinskis_2024_toward,
+ author = {Celinskis, Dmitrijs and Black, Christopher J. and Murphy, Jeremy and Barrios-Anderson, Adriel and Friedman, Nina G. and Shaner, Nathan C. and Saab, Carl Y. and Gomez-Ramirez, Manuel and Borton, David A. and Moore, Christopher I.},
+ doi = {10.1117/1.nph.11.2.024209},
+ issn = {2329-423X},
+ journal = {Neurophotonics},
+ month = {May},
+ number = {02},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {SPIE-Intl Soc Optical Eng},
+ title = {Toward a brighter constellation: multiorgan neuroimaging of neural and vascular dynamics in the spinal cord and brain},
+ url = {http://dx.doi.org/10.1117/1.nph.11.2.024209},
+ volume = {11},
+ year = {2024}
+}
+
+@article{chang_2021_behavioral,
+ author = {Chang, Chia-Jung and Guo, Wei and Zhang, Jie and Newman, Jon and Sun, Shao-Hua and Wilson, Matt},
+ doi = {10.1101/2021.04.15.440055},
+ month = {April},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Behavioral clusters revealed by end-to-end decoding from microendoscopic imaging},
+ url = {http://dx.doi.org/10.1101/2021.04.15.440055},
+ year = {2021}
+}
+
+@article{chen_2022_advances,
+ author = {Chen, Kunpeng and Tian, Zhaoshi and Kong, Lingjie},
+ doi = {10.3389/fnins.2022.994079},
+ issn = {1662-453X},
+ journal = {Frontiers in Neuroscience},
+ month = {September},
+ paper_type = {Review},
+ project = {Miniscope V4},
+ publisher = {Frontiers Media SA},
+ title = {Advances of optical miniscopes for in vivo imaging of neural activity in freely moving animals},
+ url = {http://dx.doi.org/10.3389/fnins.2022.994079},
+ volume = {16},
+ year = {2022}
+}
+
+@article{chen_2023_ensemblespecific,
+ author = {Chen, Lingxuan and Francisco, Taylor R. and Baggetta, Austin M. and Zaki, Yosif and Ramirez, Steve and Clem, Roger L. and Shuman, Tristan and Cai, Denise J.},
+ doi = {10.1016/j.neurobiolaging.2022.12.007},
+ issn = {0197-4580},
+ journal = {Neurobiology of Aging},
+ keywords = {Aging, Ensemble Tagging},
+ month = {March},
+ pages = {92–97},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Ensemble-specific deficit in neuronal intrinsic excitability in aged mice},
+ url = {http://dx.doi.org/10.1016/j.neurobiolaging.2022.12.007},
+ volume = {123},
+ year = {2023}
+}
+
+@article{chen_2022_longitudinal,
+ author = {Chen, Hao-Shan and Qiu, Shou and Wang, Guang-Ling and Yang, Rong-Rong and Zhang, Na and Wu, Jin-Ni and Yang, Qi-Xin and Xu, Chun},
+ doi = {10.1101/2022.02.05.479215},
+ month = {February},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {A longitudinal CA2/3 to CA1 circuit for initiating context-dependent associative learning},
+ url = {http://dx.doi.org/10.1101/2022.02.05.479215},
+ year = {2022}
+}
+
+@article{chen_2023_distinct,
+ author = {Chen, Gaowei and Lai, Shishi and Bao, Guo and Ke, Jincan and Meng, Xiaogao and Lu, Shanshan and Wu, Xiaocong and Xu, Hua and Wu, Fengyi and Xu, Yu and Xu, Fang and Bi, Guo-Qiang and Peng, Guangdun and Zhou, Kuikui and Zhu, Yingjie},
+ doi = {10.1016/j.celrep.2023.112069},
+ issn = {2211-1247},
+ journal = {Cell Reports},
+ keywords = {Reward, Nucleus Accumbens},
+ month = {February},
+ number = {2},
+ pages = {112069},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Elsevier BV},
+ title = {Distinct reward processing by subregions of the nucleus accumbens},
+ url = {http://dx.doi.org/10.1016/j.celrep.2023.112069},
+ volume = {42},
+ year = {2023}
+}
+
+@article{chen_2023_hardware,
+ author = {Chen, Zhe and Blair, Garrett J and Guo, Changliang and Zhou, Jim and Romero-Sosa, Juan-Luis and Izquierdo, Alicia and Golshani, Peyman and Cong, Jason and Aharoni, Daniel and Blair, Hugh T},
+ doi = {10.7554/elife.78344},
+ issn = {2050-084X},
+ journal = {eLife},
+ keywords = {Calcium Imaging},
+ month = {January},
+ project = {Miniscope V4},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {A hardware system for real-time decoding of in vivo calcium imaging data},
+ url = {http://dx.doi.org/10.7554/elife.78344},
+ volume = {12},
+ year = {2023}
+}
+
+@article{chen_2023_implementation,
+ author = {Chen, Qingyu and Son, Jeonghwan and Jia, Shu},
+ doi = {10.1364/ao.483279},
+ issn = {2155-3165},
+ journal = {Applied Optics},
+ month = {March},
+ number = {10},
+ pages = {2456},
+ project = {Miniscope DAQ},
+ publisher = {Optica Publishing Group},
+ title = {Implementation of miniaturized modular-array fluorescence microscopy for long-term live-cell imaging},
+ url = {http://dx.doi.org/10.1364/ao.483279},
+ volume = {62},
+ year = {2023}
+}
+
+@article{chen_2024_decoding,
+ author = {Chen, Yingying and Fu, Haoying and Korada, Amith and Lange, Michal A. and Rayanki, Chandrashekar and Lu, Tao and Lai, Dongbing and Fang, Shiaofen and Guo, Changyong and Ma, Yao-Ying},
+ doi = {10.1101/2024.05.20.594996},
+ month = {May},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Decoding Secondary Motor Cortex Neuronal Activity during Cocaine Self-Administration: Insights from Longitudinal
+in vivo
+Calcium Imaging},
+ url = {http://dx.doi.org/10.1101/2024.05.20.594996},
+ year = {2024}
+}
+
+@article{choi_2021_distributed,
+ author = {Choi, Kyuhyun and Piasini, Eugenio and Cifuentes-Vargas, Luigim and Díaz-Hernández, Edgar and Henderson, Nathan T. and Subramaniyan, Manivannan and Gerfen, Charles R. and Fuccillo, Marc V.},
+ doi = {10.1101/2021.12.01.469698},
+ month = {December},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Distributed processing for action control by prelimbic circuits targeting anterior-posterior dorsal striatal subregions},
+ url = {http://dx.doi.org/10.1101/2021.12.01.469698},
+ year = {2021}
+}
+
+@article{choi_2023_distributed,
+ author = {Choi, Kyuhyun and Piasini, Eugenio and Díaz-Hernández, Edgar and Cifuentes, Luigim Vargas and Henderson, Nathan T. and Holly, Elizabeth N. and Subramaniyan, Manivannan and Gerfen, Charles R. and Fuccillo, Marc V.},
+ doi = {10.1038/s41467-023-36795-4},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Reward, Neural Circuits},
+ month = {April},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Distributed processing for value-based choice by prelimbic circuits targeting anterior-posterior dorsal striatal subregions in male mice},
+ url = {http://dx.doi.org/10.1038/s41467-023-36795-4},
+ volume = {14},
+ year = {2023}
+}
+
+@article{chowdhury_2022_locus,
+ author = {Chowdhury, Ananya and Luchetti, Alessandro and Fernandes, Giselle and Filho, Daniel Almeida and Kastellakis, George and Tzilivaki, Alexandra and Ramirez, Erica M. and Tran, Mary Y. and Poirazi, Panayiota and Silva, Alcino J.},
+ doi = {10.1016/j.neuron.2022.08.001},
+ issn = {0896-6273},
+ journal = {Neuron},
+ keywords = {Hippocampus, Dopamine, Locus Coeruleus},
+ month = {October},
+ number = {20},
+ pages = {3374-3388.e8},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {A locus coeruleus-dorsal CA1 dopaminergic circuit modulates memory linking},
+ url = {http://dx.doi.org/10.1016/j.neuron.2022.08.001},
+ volume = {110},
+ year = {2022}
+}
+
+@article{erofeev_2024_integration,
+ author = {Erofeev, A. I. and Vinokurov, E. K. and Antifeev, I. E. and Vlasova, O. L. and Bezprozvanny, I. B.},
+ doi = {10.1134/s0022093024040264},
+ issn = {1608-3202},
+ journal = {Journal of Evolutionary Biochemistry and Physiology},
+ keywords = {Calcium Imaging, Hippocampus, Electrophysiology},
+ month = {July},
+ number = {4},
+ pages = {1586–1606},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Pleiades Publishing Ltd},
+ title = {Integration of Single-Photon Miniature Fluorescence Microscopy and Electrophysiological Recording Methods for in vivo Studying Hippocampal Neuronal Activity},
+ url = {http://dx.doi.org/10.1134/s0022093024040264},
+ volume = {60},
+ year = {2024}
+}
+
+@article{erofeev_2024_optimizing,
+ author = {Erofeev, A. I. and Petrushan, M. V. and Lysenko, L. V. and Vinokurov, E. K. and Vlasova, O. L. and Bezprozvanny, I. B.},
+ doi = {10.1007/s11055-024-01593-y},
+ issn = {1573-899X},
+ journal = {Neuroscience and Behavioral Physiology},
+ month = {February},
+ number = {2},
+ pages = {251–262},
+ project = {Minian},
+ publisher = {Springer Science and Business Media LLC},
+ title = {On Optimizing Miniscope Data Analysis with Simulated Data: A Study of Parameter Optimization in the Minian Analysis Pipeline},
+ url = {http://dx.doi.org/10.1007/s11055-024-01593-y},
+ volume = {54},
+ year = {2024}
+}
+
+@article{aseyev_2024_cadence,
+ author = {Aseyev, Nikolay and Borodinova, Anastasia and Pavlova, Svetlana and Roshchina, Marina and Roshchin, Matvey and Nikitin, Evgeny and Balaban, Pavel},
+ doi = {10.1007/s12021-024-09677-3},
+ issn = {1559-0089},
+ journal = {Neuroinformatics},
+ keywords = {Calcium Imaging, Open-Source},
+ month = {July},
+ number = {3},
+ pages = {379–387},
+ paper_type = {Analysis Pipeline},
+ publisher = {Springer Science and Business Media LLC},
+ title = {CADENCE — Neuroinformatics Tool for Supervised Calcium Events Detection},
+ url = {http://dx.doi.org/10.1007/s12021-024-09677-3},
+ volume = {22},
+ year = {2024}
+}
+
+@article{barry_2022_dissociable,
+ author = {Barry, Joshua and Oikonomou, Katerina D. and Peng, Allison and Yu, Daniel and Yang, Chenyi and Golshani, Peyman and Evans, Christopher J. and Levine, Michael S. and Cepeda, Carlos},
+ doi = {10.3389/fncir.2022.983323},
+ issn = {1662-5110},
+ journal = {Frontiers in Neural Circuits},
+ keywords = {Electrophysiology},
+ month = {October},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Frontiers Media SA},
+ title = {Dissociable effects of oxycodone on behavior, calcium transient activity, and excitability of dorsolateral striatal neurons},
+ url = {http://dx.doi.org/10.3389/fncir.2022.983323},
+ volume = {16},
+ year = {2022}
+}
+
+@article{berigan_2023_imaging,
+ author = {Berigan, Benton R. and Wang, Jing and Schulz, David J. and Ozden, Ilker},
+ doi = {10.1152/jn.00450.2022},
+ issn = {1522-1598},
+ journal = {Journal of Neurophysiology},
+ keywords = {Calcium Imaging},
+ month = {February},
+ number = {2},
+ pages = {479–493},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {American Physiological Society},
+ title = {Imaging neuro-urodynamics of mouse major pelvic ganglion with a micro-endoscopic approach},
+ url = {http://dx.doi.org/10.1152/jn.00450.2022},
+ volume = {129},
+ year = {2023}
+}
+
+@article{borkar_2024_topdown,
+ author = {Borkar, Chandrashekhar D. and Stelly, Claire E. and Fu, Xin and Dorofeikova, Maria and Le, Quan-Son Eric and Vutukuri, Rithvik and Vo, Catherine and Walker, Alice Breaux and Basavanhalli, Samhita and Duong, Anh and Bean, Erin and Resendez, Alexis and Parker, Jones G. and Tasker, Jeffrey G. and Fadok, Jonathan P.},
+ doi = {10.1038/s41586-023-06912-w},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Amygdala, Prefrontal Cortex, Neural Circuits},
+ month = {January},
+ number = {7996},
+ pages = {743–749},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Top-down control of flight by a non-canonical cortico-amygdala pathway},
+ url = {http://dx.doi.org/10.1038/s41586-023-06912-w},
+ volume = {625},
+ year = {2024}
+}
+
+@article{bowles_2021_vagus,
+ author = {Bowles, Spencer and Hickman, Jordan and Peng, Xiaoyu and Williamson, W. Ryan and Huang, Rongchen and Washington, Kayden and Donegan, Dane and Welle, Cristin G},
+ doi = {10.1101/2021.10.28.466306},
+ month = {October},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Vagus nerve stimulation accelerates motor learning through cholinergic modulation},
+ url = {http://dx.doi.org/10.1101/2021.10.28.466306},
+ year = {2021}
+}
+
+@article{bowles_2022_vagus,
+ author = {Bowles, Spencer and Hickman, Jordan and Peng, Xiaoyu and Williamson, W. Ryan and Huang, Rongchen and Washington, Kayden and Donegan, Dane and Welle, Cristin G.},
+ doi = {10.1016/j.neuron.2022.06.017},
+ issn = {0896-6273},
+ journal = {Neuron},
+ month = {September},
+ number = {17},
+ pages = {2867–2885.e7},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Vagus nerve stimulation drives selective circuit modulation through cholinergic reinforcement},
+ url = {http://dx.doi.org/10.1016/j.neuron.2022.06.017},
+ volume = {110},
+ year = {2022}
+}
+
+@article{carrasco_2024_monthslong,
+ author = {Carrasco, Sofia Skromne and Viejo, Guillaume and Peyrache, Adrien},
+ doi = {10.1101/2024.06.13.598909},
+ month = {June},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Months-long stability of the head-direction system},
+ url = {http://dx.doi.org/10.1101/2024.06.13.598909},
+ year = {2024}
+}
+
+@article{skromne_carrasco_2026_monthslong,
+ author = {Skromne Carrasco, Sofia and Viejo, Guillaume and Peyrache, Adrien},
+ doi = {10.1038/s41586-025-10096-w},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Memory, Neural Circuits},
+ month = {February},
+ number = {8108},
+ pages = {167–173},
+ project = {Miniscope V4},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Months-long stability of the head-direction system},
+ url = {http://dx.doi.org/10.1038/s41586-025-10096-w},
+ volume = {652},
+ year = {2026}
+}
+
+@inproceedings{chen_2021_fast,
+ author = {Chen, Zhe and Blair, Garrett J. and Blair, Hugh T. and Cong, Jason},
+ booktitle = {2021 IEEE Biomedical Circuits and Systems Conference (BioCAS)},
+ doi = {10.1109/biocas49922.2021.9644936},
+ month = {October},
+ pages = {1–5},
+ project = {MiniLFOV},
+ publisher = {IEEE},
+ title = {Fast Calcium Trace Extraction for Large-Field-of-View Miniscope},
+ url = {http://dx.doi.org/10.1109/biocas49922.2021.9644936},
+ year = {2021}
+}
+
+@article{chen_2022_circuit,
+ author = {Chen, Zijun and Chen, Gaowei and Zhong, Jiafeng and Jiang, Shaolei and Lai, Shishi and Xu, Hua and Deng, Xiaofei and Li, Fengling and Lu, Shanshan and Zhou, Kuikui and Li, Changlin and Liu, Zhongdong and Zhang, Xu and Zhu, Yingjie},
+ doi = {10.1038/s41380-022-01742-0},
+ issn = {1476-5578},
+ journal = {Molecular Psychiatry},
+ month = {August},
+ number = {12},
+ pages = {4843–4860},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Springer Science and Business Media LLC},
+ title = {A circuit from lateral septum neurotensin neurons to tuberal nucleus controls hedonic feeding},
+ url = {http://dx.doi.org/10.1038/s41380-022-01742-0},
+ volume = {27},
+ year = {2022}
+}
+
+@article{chen_2022_ubiquitous,
+ author = {Chen, Yi-Ling and Chen, Chun-Chung and Mei, Yu-Ying and Zhou, Ning and Wu, Dongchuan and Lee, Ting-Kuo},
+ doi = {10.1016/j.cjph.2021.12.010},
+ issn = {0577-9073},
+ journal = {Chinese Journal of Physics},
+ keywords = {Hippocampus},
+ month = {June},
+ pages = {497–510},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Ubiquitous proximity to a critical state for collective neural activity in the CA1 region of freely moving mice},
+ url = {http://dx.doi.org/10.1016/j.cjph.2021.12.010},
+ volume = {77},
+ year = {2022}
+}
+
+@article{chung_2021_cognitive,
+ author = {Chung, Ain and Jou, Claudia and Grau-Perales, Alejandro and Levy, Eliott R. J. and Dvorak, Dino and Hussain, Nida and Fenton, André A.},
+ doi = {10.1038/s41586-021-04070-5},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Hippocampus, Memory},
+ month = {November},
+ number = {7889},
+ pages = {484–488},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Cognitive control persistently enhances hippocampal information processing},
+ url = {http://dx.doi.org/10.1038/s41586-021-04070-5},
+ volume = {600},
+ year = {2021}
+}
+
+@article{dong_2025_simultaneous,
+ author = {Dong, Zhe and Feng, Yu and Diego, Keziah and Baggetta, Austin M. and Sweis, Brian M. and Pennington, Zachary T. and Lamsifer, Sophia I. and Zaki, Yosif and Sangiuliano, Federico and Philipsberg, Paul A. and Morales-Rodriguez, Denisse and Kircher, Daniel and Slesinger, Paul and Shuman, Tristan and Aharoni, Daniel and Cai, Denise J.},
+ doi = {10.1126/sciadv.adr6470},
+ issn = {2375-2548},
+ journal = {Science Advances},
+ keywords = {Calcium Imaging, Hippocampus, Place Cells, Open-Source, Freely-Behaving},
+ month = {July},
+ number = {27},
+ paper_type = {Tool Paper},
+ project = {Miniscope V4},
+ publisher = {American Association for the Advancement of Science (AAAS)},
+ title = {Simultaneous two-color imaging with a dual-channel miniscope in freely behaving mice},
+ url = {http://dx.doi.org/10.1126/sciadv.adr6470},
+ volume = {11},
+ year = {2025}
+}
+
+@article{etter_2020_probabilistic,
+ author = {Etter, Guillaume and Manseau, Frederic and Williams, Sylvain},
+ doi = {10.3389/fncir.2020.00019},
+ issn = {1662-5110},
+ journal = {Frontiers in Neural Circuits},
+ keywords = {Calcium Imaging, Hippocampus},
+ month = {May},
+ project = {Miniscope V3},
+ publisher = {Frontiers Media SA},
+ title = {A Probabilistic Framework for Decoding Behavior From in vivo Calcium Imaging Data},
+ url = {http://dx.doi.org/10.3389/fncir.2020.00019},
+ volume = {14},
+ year = {2020}
+}
+
+@article{etter_2023_optogenetic,
+ author = {Etter, Guillaume and van der Veldt, Suzanne and Choi, Jisoo and Williams, Sylvain},
+ doi = {10.1038/s41467-023-35825-5},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Hippocampus, Neural Circuits},
+ month = {January},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Optogenetic frequency scrambling of hippocampal theta oscillations dissociates working memory retrieval from hippocampal spatiotemporal codes},
+ url = {http://dx.doi.org/10.1038/s41467-023-35825-5},
+ volume = {14},
+ year = {2023}
+}
+
+@article{etter_2023_population,
+ author = {Etter, Guillaume and van der Veldt, Suzanne and Mosser, Coralie-Anne and Hasselmo, Michael E and Williams, Sylvain},
+ doi = {10.1101/2023.11.10.566641},
+ month = {November},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {A population code for idiothetic representations in the hippocampal-septal circuit},
+ url = {http://dx.doi.org/10.1101/2023.11.10.566641},
+ year = {2023}
+}
+
+@article{farrell_2021_midbrain,
+ author = {Farrell, Karolina and Lak, Armin and Saleem, Aman B},
+ doi = {10.1101/2021.02.17.431585},
+ month = {February},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Midbrain dopamine neurons provide teaching signals for goal-directed navigation},
+ url = {http://dx.doi.org/10.1101/2021.02.17.431585},
+ year = {2021}
+}
+
+@article{feng_2024_distinct,
+ author = {Feng, Yu and Diego, Keziah S. and Dong, Zhe and Wick, Zoé Christenson and Page-Harley, Lucia and Page-Harley, Veronica and Schnipper, Julia and Lamsifer, Sophia I. and Pennington, Zachary T. and Vetere, Lauren M. and Philipsberg, Paul A. and Soler, Ivan and Jurkowski, Albert and Rosado, Christin J. and Khan, Nadia N. and Cai, Denise J. and Shuman, Tristan},
+ doi = {10.1101/2024.03.12.584697},
+ month = {March},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Distinct changes to hippocampal and medial entorhinal circuits emerge across the progression of cognitive deficits in epilepsy},
+ url = {http://dx.doi.org/10.1101/2024.03.12.584697},
+ year = {2024}
+}
+
+@article{froula_2024_distinct,
+ author = {Froula, Jessica M. and Rose, Jarrett J and Krook-Magnuson, Chris and Krook-Magnuson, Esther},
+ doi = {10.1101/2024.05.14.594213},
+ month = {May},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Distinct functional classes of CA1 hippocampal interneurons are modulated by cerebellar stimulation in a coordinated manner},
+ url = {http://dx.doi.org/10.1101/2024.05.14.594213},
+ year = {2024}
+}
+
+@article{gabriel_2022_behaviordepot,
+ author = {Gabriel, Christopher J and Zeidler, Zachary and Jin, Benita and Guo, Changliang and Goodpaster, Caitlin M and Kashay, Adrienne Q and Wu, Anna and Delaney, Molly and Cheung, Jovian and DiFazio, Lauren E and Sharpe, Melissa J and Aharoni, Daniel and Wilke, Scott A and DeNardo, Laura A},
+ doi = {10.7554/elife.74314},
+ issn = {2050-084X},
+ journal = {eLife},
+ month = {August},
+ project = {Miniscope V3},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking},
+ url = {http://dx.doi.org/10.7554/elife.74314},
+ volume = {11},
+ year = {2022}
+}
+
+@article{gagliardi_2024_distinct,
+ author = {Gagliardi, Celia M. and Normandin, Marc E. and Keinath, Alexandra T. and Julian, Joshua B. and Lopez, Matthew R. and Ramos-Alvarez, Manuel-Miguel and Epstein, Russell A. and Muzzio, Isabel A.},
+ doi = {10.1038/s41467-024-50112-7},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Hippocampus, Place Cells, Spatial Navigation},
+ month = {July},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Distinct neural mechanisms for heading retrieval and context recognition in the hippocampus during spatial reorientation},
+ url = {http://dx.doi.org/10.1038/s41467-024-50112-7},
+ volume = {15},
+ year = {2024}
+}
+
+@inproceedings{gao_2020_novel,
+ author = {Gao, Sibo and Webb, James and Mridha, Zakir and Banta, Anton and Kemere, Caleb and McGinley, Matthew},
+ booktitle = {2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)},
+ doi = {10.1109/embc44109.2020.9176536},
+ keywords = {Hippocampus, Spatial Navigation, Calcium Imaging},
+ month = {July},
+ pages = {2925–2928},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {IEEE},
+ title = {Novel Virtual Reality System for Auditory Tasks in Head-fixed Mice},
+ url = {http://dx.doi.org/10.1109/embc44109.2020.9176536},
+ year = {2020}
+}
+
+@article{grieco_2020_subanesthetic,
+ author = {Grieco, Steven F. and Qiao, Xin and Zheng, Xiaoting and Liu, Yongjun and Chen, Lujia and Zhang, Hai and Yu, Zhaoxia and Gavornik, Jeffrey P. and Lai, Cary and Gandhi, Sunil P. and Holmes, Todd C. and Xu, Xiangmin},
+ doi = {10.1016/j.cub.2020.07.008},
+ issn = {0960-9822},
+ journal = {Current Biology},
+ keywords = {Electrophysiology},
+ month = {September},
+ number = {18},
+ pages = {3591-3603.e8},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Subanesthetic Ketamine Reactivates Adult Cortical Plasticity to Restore Vision from Amblyopia},
+ url = {http://dx.doi.org/10.1016/j.cub.2020.07.008},
+ volume = {30},
+ year = {2020}
+}
+
+@article{grieco_2021_neuregulin,
+ author = {Grieco, Steven F. and Qiao, Xin and Johnston, Kevin G. and Chen, Lujia and Nelson, Renetta R. and Lai, Cary and Holmes, Todd C. and Xu, Xiangmin},
+ doi = {10.1038/s41398-021-01255-4},
+ issn = {2158-3188},
+ journal = {Translational Psychiatry},
+ month = {February},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Neuregulin signaling mediates the acute and sustained antidepressant effects of subanesthetic ketamine},
+ url = {http://dx.doi.org/10.1038/s41398-021-01255-4},
+ volume = {11},
+ year = {2021}
+}
+
+@article{de_groot_2020_ninscope,
+ author = {de Groot, Andres and van den Boom, Bastijn JG and van Genderen, Romano M and Coppens, Joris and van Veldhuijzen, John and Bos, Joop and Hoedemaker, Hugo and Negrello, Mario and Willuhn, Ingo and De Zeeuw, Chris I and Hoogland, Tycho M},
+ doi = {10.7554/elife.49987},
+ issn = {2050-084X},
+ journal = {eLife},
+ month = {January},
+ project = {Miniscope V4},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {NINscope, a versatile miniscope for multi-region circuit investigations},
+ url = {http://dx.doi.org/10.7554/elife.49987},
+ volume = {9},
+ year = {2020}
+}
+
+@article{guo_2020_latent,
+ author = {Guo, Wei and Zhang, Jie J. and Newman, Jonathan P. and Wilson, Matthew A.},
+ doi = {10.1101/2020.02.27.967794},
+ month = {February},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Latent learning drives sleep-dependent plasticity in distinct CA1 subpopulations},
+ url = {http://dx.doi.org/10.1101/2020.02.27.967794},
+ year = {2020}
+}
+
+@article{guo_2022_new,
+ author = {Guo, Changliang and Wang, Aimin and Cheng, Heping and Chen, Liangyi},
+ doi = {10.1111/jnc.15711},
+ issn = {1471-4159},
+ journal = {Journal of Neurochemistry},
+ keywords = {Two-Photon},
+ month = {November},
+ number = {3},
+ pages = {270–283},
+ paper_type = {Review},
+ project = {MiniLFOV},
+ publisher = {Wiley},
+ title = {New imaging instrument in animal models: Two‐photon miniature microscope and large field of view miniature microscope for freely behaving animals},
+ url = {http://dx.doi.org/10.1111/jnc.15711},
+ volume = {164},
+ year = {2022}
+}
+
+@article{habibollahi_2023_neural,
+ author = {Habibollahi, Forough and Sun, Dechuan and Burkitt, Anthony N. and French, Chris},
+ doi = {10.1101/2023.08.16.553626},
+ month = {August},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Neural Networks Are Tuned Near Criticality During a Cognitive Task and Distanced from Criticality In a Psychopharmacological Model of Alzheimer’s Disease},
+ url = {http://dx.doi.org/10.1101/2023.08.16.553626},
+ year = {2023}
+}
+
+@article{han_2023_mechanism,
+ author = {Han, Su Young and Morris, Paul G. and Kim, Jae-Chang and Guru, Santosh and Pardo-Navarro, Maria and Yeo, Shel-Hwa and McQuillan, H. James and Herbison, Allan E.},
+ doi = {10.1016/j.celrep.2022.111914},
+ issn = {2211-1247},
+ journal = {Cell Reports},
+ month = {January},
+ number = {1},
+ pages = {111914},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Elsevier BV},
+ title = {Mechanism of kisspeptin neuron synchronization for pulsatile hormone secretion in male mice},
+ url = {http://dx.doi.org/10.1016/j.celrep.2022.111914},
+ volume = {42},
+ year = {2023}
+}
+
+@article{hart_2020_chemogenetic,
+ author = {Hart, Evan E. and Blair, Garrett J. and O’Dell, Thomas J. and Blair, Hugh T. and Izquierdo, Alicia},
+ doi = {10.1523/jneurosci.2548-19.2020},
+ issn = {1529-2401},
+ journal = {The Journal of Neuroscience},
+ keywords = {Calcium Imaging},
+ month = {June},
+ number = {29},
+ pages = {5628–5643},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Society for Neuroscience},
+ title = {Chemogenetic Modulation and Single-Photon Calcium Imaging in Anterior Cingulate Cortex Reveal a Mechanism for Effort-Based Decisions},
+ url = {http://dx.doi.org/10.1523/jneurosci.2548-19.2020},
+ volume = {40},
+ year = {2020}
+}
+
+@article{hart_2022_calcium,
+ author = {Hart, Evan E. and Gardner, Matthew P.H. and Panayi, Marios C. and Kahnt, Thorsten and Schoenbaum, Geoffrey},
+ doi = {10.1016/j.cub.2022.10.037},
+ issn = {0960-9822},
+ journal = {Current Biology},
+ keywords = {Calcium Imaging, Reward, Electrophysiology},
+ month = {December},
+ number = {24},
+ pages = {5364-5373.e4},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Calcium activity is a degraded estimate of spikes},
+ url = {http://dx.doi.org/10.1016/j.cub.2022.10.037},
+ volume = {32},
+ year = {2022}
+}
+
+@article{hayashi_2021_largescale,
+ author = {Hayashi, Yuichiro and Kobayakawa, Ko and Kobayakawa, Reiko},
+ doi = {10.1101/2021.01.20.427512},
+ month = {January},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Large-scale calcium imaging with a head-mounted axial scanning 3D fluorescence microscope},
+ url = {http://dx.doi.org/10.1101/2021.01.20.427512},
+ year = {2021}
+}
+
+@article{hayashi_2023_temporal,
+ author = {Hayashi, Yuichiro and Kobayakawa, Ko and Kobayakawa, Reiko},
+ doi = {10.1073/pnas.2221141120},
+ issn = {1091-6490},
+ journal = {Proceedings of the National Academy of Sciences},
+ month = {April},
+ number = {17},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Proceedings of the National Academy of Sciences},
+ title = {The temporal and contextual stability of activity levels in hippocampal CA1 cells},
+ url = {http://dx.doi.org/10.1073/pnas.2221141120},
+ volume = {120},
+ year = {2023}
+}
+
+@article{hirano_2022_impact,
+ author = {Hirano, Kyosuke and Morishita, Yoshikazu and Minami, Masabumi and Nomura, Hiroshi},
+ doi = {10.1038/s41598-022-11032-y},
+ issn = {2045-2322},
+ journal = {Scientific Reports},
+ keywords = {Memory},
+ month = {May},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {The impact of pitolisant, an H3 receptor antagonist/inverse agonist, on perirhinal cortex activity in individual neuron and neuronal population levels},
+ url = {http://dx.doi.org/10.1038/s41598-022-11032-y},
+ volume = {12},
+ year = {2022}
+}
+
+@article{hsiao_2021_using,
+ author = {Hsiao, Yi-Tse and Wang, Angela Yu-Chi and Lee, Ting-Yen and Chang, Ching-Yuan},
+ doi = {10.3791/62611},
+ issn = {1940-087X},
+ journal = {Journal of Visualized Experiments},
+ month = {June},
+ number = {172},
+ paper_type = {Protocol},
+ project = {Miniscope V3},
+ publisher = {MyJove Corporation},
+ title = {Using Baseplating and a Miniscope Preanchored with an Objective Lens for Calcium Transient Research in Mice},
+ url = {http://dx.doi.org/10.3791/62611},
+ year = {2021}
+}
+
+@article{huerta_2023_calcium,
+ author = {Huerta, Tomás S and Haider, Bilal and Adamovich-Zeitlin, Richard and Chen, Adrian C and Chaudhry, Saher and Zanos, Theodoros P and Chavan, Sangeeta S and Tracey, Kevin J and Chang, Eric H},
+ doi = {10.1088/1741-2552/acbe1e},
+ issn = {1741-2552},
+ journal = {Journal of Neural Engineering},
+ month = {March},
+ number = {2},
+ pages = {026014},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {IOP Publishing},
+ title = {Calcium imaging and analysis of the jugular-nodose ganglia enables identification of distinct vagal sensory neuron subsets},
+ url = {http://dx.doi.org/10.1088/1741-2552/acbe1e},
+ volume = {20},
+ year = {2023}
+}
+
+@article{hughes_2019_precise,
+ author = {Hughes, Ryan N. and Watson, Glenn D.R. and Petter, Elijah A. and Kim, Namsoo and Bakhurin, Konstantin I. and Yin, Henry H.},
+ doi = {10.1016/j.cub.2019.08.022},
+ issn = {0960-9822},
+ journal = {Current Biology},
+ month = {October},
+ number = {19},
+ pages = {3244-3255.e4},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Precise Coordination of Three-Dimensional Rotational Kinematics by Ventral Tegmental Area GABAergic Neurons},
+ url = {http://dx.doi.org/10.1016/j.cub.2019.08.022},
+ volume = {29},
+ year = {2019}
+}
+
+@article{hur_2024_correlated,
+ author = {Hur, Sung Won and Safaryan, Karen and Yang, Long and Blair, Hugh T and Masmanidis, Sotiris C and Mathews, Paul J and Aharoni, Daniel and Golshani, Peyman},
+ doi = {10.7554/elife.88439},
+ issn = {2050-084X},
+ journal = {eLife},
+ keywords = {Social Behavior},
+ month = {February},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {Correlated signatures of social behavior in cerebellum and anterior cingulate cortex},
+ url = {http://dx.doi.org/10.7554/elife.88439},
+ volume = {12},
+ year = {2024}
+}
+
+@article{jameson_2023_vagal,
+ author = {Jameson, Kelly G. and Kazmi, Sabeen A. and Son, Celine and Mazdeyasnan, Donya and Leshan, Emma and Vuong, Helen E. and Paramo, Jorge and Lopez-Romero, Arlene and Yang, Long and Schweizer, Felix E. and Hsiao, Elaine Y.},
+ doi = {10.1101/2023.12.18.572257},
+ month = {December},
+ paper_type = {Science},
+ project = {Minian},
+ publisher = {openRxiv},
+ title = {Vagal interoception of microbial metabolites from the small intestinal lumen},
+ url = {http://dx.doi.org/10.1101/2023.12.18.572257},
+ year = {2023}
+}
+
+@article{jendryka_2024_excitatory,
+ author = {Jendryka, Martin M. and Lewin, Uwe and Kapanaiah, Sampath K.T. and Dermutz, Hartmut and Liss, Birgit and Pekcec, Anton and Akam, Thomas and Grewe, Benjamin F. and Kätzel, Dennis},
+ doi = {10.1101/2024.04.12.589244},
+ month = {April},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Excitatory neurons of the anterior cingulate cortex encode chosen actions and their outcomes rather than cognitive state},
+ url = {http://dx.doi.org/10.1101/2024.04.12.589244},
+ year = {2024}
+}
+
+@article{johnson_2022_highly,
+ author = {Johnson, Connor and Kretsge, Lisa N. and Yen, William W. and Sriram, Balaji and O’Connor, Alexandra and Liu, Ruichen Sky and Jimenez, Jessica C. and Phadke, Rhushikesh A. and Wingfield, Kelly K. and Yeung, Charlotte and Jinadasa, Tushare J. and Nguyen, Thanh P. H. and Cho, Eun Seon and Fuchs, Erelle and Spevack, Eli D. and Velasco, Berta Escude and Hausmann, Frances S. and Fournier, Luke A. and Brack, Alison and Melzer, Sarah and Cruz-Martín, Alberto},
+ doi = {10.1038/s41380-022-01485-y},
+ issn = {1476-5578},
+ journal = {Molecular Psychiatry},
+ keywords = {Prefrontal Cortex, Fear & Anxiety, Social Behavior, Calcium Imaging},
+ month = {March},
+ number = {5},
+ pages = {2602–2618},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Highly unstable heterogeneous representations in VIP interneurons of the anterior cingulate cortex},
+ url = {http://dx.doi.org/10.1038/s41380-022-01485-y},
+ volume = {27},
+ year = {2022}
+}
+
+@article{johnston_2020_robust,
+ author = {Johnston, Kevin G. and Grieco, Steven F. and Yu, Zhaoxia and Jin, Suoqin and Shen, Tong and Crary, Rachel and Guzowski, John F. and Holmes, Todd C. and Nie, Qing and Xu, Xiangmin},
+ doi = {10.1101/2020.08.26.268151},
+ month = {August},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Robust Population Single Neuronal Calcium Signal Extraction Using SCOUT Allows for Longitudinal Analysis of Behavior-associated Neural Ensemble Dynamics},
+ url = {http://dx.doi.org/10.1101/2020.08.26.268151},
+ year = {2020}
+}
+
+@article{johnston_2022_tracking,
+ author = {Johnston, Kevin G. and Grieco, Steven F. and Zhang, Hai and Jin, Suoqin and Xu, Xiangmin and Nie, Qing},
+ doi = {10.1016/j.crmeth.2022.100207},
+ issn = {2667-2375},
+ journal = {Cell Reports Methods},
+ keywords = {Calcium Imaging},
+ month = {May},
+ number = {5},
+ pages = {100207},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT},
+ url = {http://dx.doi.org/10.1016/j.crmeth.2022.100207},
+ volume = {2},
+ year = {2022}
+}
+
+@inproceedings{juneau_2018_enhanced,
+ author = {Juneau, Jill and Duret, Guillaume and Robinson, Jacob and Kemere, Caleb},
+ booktitle = {2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)},
+ doi = {10.1109/embc.2018.8512387},
+ month = {July},
+ pages = {826–829},
+ project = {Miniscope V3},
+ publisher = {IEEE},
+ title = {Enhanced Image Sensor Module for Head-Mounted Microscopes},
+ url = {http://dx.doi.org/10.1109/embc.2018.8512387},
+ year = {2018}
+}
+
+@article{juneau_2020_minifast,
+ author = {Juneau, Jill and Duret, Guillaume and Chu, Joshua and Rodriguez, Alex and Morozov, Savva and Aharoni, Daniel and Robinson, Jacob and St-Pierre, Francois and Kemere, Caleb and Golshani, Peyman and Dorian, Conor C and Madruga, Blake},
+ doi = {10.1101/2020.11.03.367466},
+ month = {November},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {MiniFAST: A sensitive and fast miniaturized microscope for in vivo neural recording},
+ url = {http://dx.doi.org/10.1101/2020.11.03.367466},
+ year = {2020}
+}
+
+@article{kaang_2023_cortical,
+ author = {Kaang, Bong-Kiun and Ko, Hyoung-Gon and Choi, Dong Il and Lee, Chiwoo and Choi, Ja Eun and Oh, Jihae and Han, Seunghyo and Ye, Sanghyun and Lee, Jiah and Jung, Hyunsu and Lee, Jaehyun and Lee, Kyungmin and Lee, Jae-Hyung and Zhuo, Min},
+ doi = {10.21203/rs.3.rs-3480103/v1},
+ month = {November},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Cortical processing of pain and itch information by distinct neuronal populations},
+ url = {http://dx.doi.org/10.21203/rs.3.rs-3480103/v1},
+ year = {2023}
+}
+
+@article{kamm_2021_synaptic,
+ author = {Kamm, Gretel B. and Boffi, Juan C. and Zuza, Kristina and Nencini, Sara and Campos, Joaquin and Schrenk-Siemens, Katrin and Sonntag, Ivo and Kabaoğlu, Burçe and El Hay, Muad Y. Abd and Schwarz, Yvonne and Tappe-Theodor, Anke and Bruns, Dieter and Acuna, Claudio and Kuner, Thomas and Siemens, Jan},
+ doi = {10.1016/j.neuron.2021.10.001},
+ issn = {0896-6273},
+ journal = {Neuron},
+ month = {October},
+ number = {20},
+ pages = {3283-3297.e11},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {A synaptic temperature sensor for body cooling},
+ url = {http://dx.doi.org/10.1016/j.neuron.2021.10.001},
+ volume = {109},
+ year = {2021}
+}
+
+@article{kapanaiah_2023_openmac,
+ author = {Kapanaiah, Sampath K.T. and Kätzel, Dennis},
+ doi = {10.1016/j.ohx.2023.e00429},
+ issn = {2468-0672},
+ journal = {HardwareX},
+ keywords = {Open-Source, Freely-Behaving, Optogenetics},
+ month = {June},
+ pages = {e00429},
+ paper_type = {Tool Paper},
+ publisher = {Elsevier BV},
+ title = {Open-MAC: A low-cost open-source motorized commutator for electro- and opto-physiological recordings in freely moving rodents},
+ url = {http://dx.doi.org/10.1016/j.ohx.2023.e00429},
+ volume = {14},
+ year = {2023}
+}
+
+@article{keinath_2020_dgca3,
+ author = {Keinath, Alexandra T. and Nieto-Posadas, Andrés and Robinson, Jennifer C. and Brandon, Mark P.},
+ doi = {10.1038/s41467-020-16825-1},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Hippocampus, Memory, Neural Circuits},
+ month = {June},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {DG–CA3 circuitry mediates hippocampal representations of latent information},
+ url = {http://dx.doi.org/10.1038/s41467-020-16825-1},
+ volume = {11},
+ year = {2020}
+}
+
+@article{keinath_2022_representation,
+ author = {Keinath, Alexandra T. and Mosser, Coralie-Anne and Brandon, Mark P.},
+ doi = {10.1038/s41467-022-30198-7},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Hippocampus, Memory},
+ month = {May},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {The representation of context in mouse hippocampus is preserved despite neural drift},
+ url = {http://dx.doi.org/10.1038/s41467-022-30198-7},
+ volume = {13},
+ year = {2022}
+}
+
+@article{kim_2019_striatal,
+ author = {Kim, Namsoo and Li, Haofang E. and Hughes, Ryan N. and Watson, Glenn D. R. and Gallegos, David and West, Anne E. and Kim, Il Hwan and Yin, Henry H.},
+ doi = {10.1038/s41467-019-10716-w},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Calcium Imaging, Reward, Neural Circuits},
+ month = {June},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {A striatal interneuron circuit for continuous target pursuit},
+ url = {http://dx.doi.org/10.1038/s41467-019-10716-w},
+ volume = {10},
+ year = {2019}
+}
+
+@article{kim_2022_simultaneous,
+ author = {Kim, Chae Young and Kim, Sang Jeong and Kloosterman, Fabian},
+ doi = {10.5607/en22011},
+ issn = {2093-8144},
+ journal = {Experimental Neurobiology},
+ month = {June},
+ number = {3},
+ pages = {208–220},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {The Korean Society for Brain and Neural Science},
+ title = {Simultaneous Cellular Imaging, Electrical Recording and Stimulation of Hippocampal Activity in Freely Behaving Mice},
+ url = {http://dx.doi.org/10.5607/en22011},
+ volume = {31},
+ year = {2022}
+}
+
+@article{kim_2023_advances,
+ author = {Kim, Su Jin and Affan, Rifqi O. and Frostig, Hadas and Scott, Benjamin B. and Alexander, Andrew S.},
+ doi = {10.1117/1.nph.10.4.044304},
+ issn = {2329-423X},
+ journal = {Neurophotonics},
+ month = {November},
+ number = {04},
+ paper_type = {Review},
+ project = {MiniLFOV},
+ publisher = {SPIE-Intl Soc Optical Eng},
+ title = {Advances in cellular resolution microscopy for brain imaging in rats},
+ url = {http://dx.doi.org/10.1117/1.nph.10.4.044304},
+ volume = {10},
+ year = {2023}
+}
+
+@article{kingsbury_2019_correlated,
+ author = {Kingsbury, Lyle and Huang, Shan and Wang, Jun and Gu, Ken and Golshani, Peyman and Wu, Ye Emily and Hong, Weizhe},
+ doi = {10.1016/j.cell.2019.05.022},
+ issn = {0092-8674},
+ journal = {Cell},
+ keywords = {Prefrontal Cortex, Social Behavior, Calcium Imaging},
+ month = {July},
+ number = {2},
+ pages = {429–446.e16},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Correlated Neural Activity and Encoding of Behavior across Brains of Socially Interacting Animals},
+ url = {http://dx.doi.org/10.1016/j.cell.2019.05.022},
+ volume = {178},
+ year = {2019}
+}
+
+@article{kingsbury_2020_cortical,
+ author = {Kingsbury, Lyle and Huang, Shan and Raam, Tara and Ye, Letizia S. and Wei, Don and Hu, Rongfeng K. and Ye, Li and Hong, Weizhe},
+ doi = {10.1016/j.neuron.2020.06.020},
+ issn = {0896-6273},
+ journal = {Neuron},
+ keywords = {Prefrontal Cortex, Social Behavior, Calcium Imaging},
+ month = {September},
+ number = {5},
+ pages = {941–953.e7},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Cortical Representations of Conspecific Sex Shape Social Behavior},
+ url = {http://dx.doi.org/10.1016/j.neuron.2020.06.020},
+ volume = {107},
+ year = {2020}
+}
+
+@article{klumpp_2025_syntalos,
+ author = {Klumpp, Matthias and Embray, Lee and Heimburg, Filippo and Alves Dias, Ana Luiza and Simon, Justus and Groh, Alexander and Draguhn, Andreas and Both, Martin},
+ doi = {10.1038/s41467-025-56081-9},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Open-Source, Multi-Region, Optogenetics},
+ month = {January},
+ number = {1},
+ paper_type = {Software},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Syntalos: a software for precise synchronization of simultaneous multi-modal data acquisition and closed-loop interventions},
+ url = {http://dx.doi.org/10.1038/s41467-025-56081-9},
+ volume = {16},
+ year = {2025}
+}
+
+@article{korzus_2024_prefrontal,
+ author = {Korzus, Edward and Pastore, Justin and Mayer, Johannes and Bailey, Tyler and III, John Speigel and Steinhauser, Jordan and Shuler, Kylene and Papalexakis, Evangelos},
+ doi = {10.21203/rs.3.rs-3908560/v1},
+ month = {January},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Prefrontal multistimulus integration within a dedicated disambiguation circuit guides interleaving contingency judgment learning},
+ url = {http://dx.doi.org/10.21203/rs.3.rs-3908560/v1},
+ year = {2024}
+}
+
+@article{de_kraker_2022_specseg,
+ author = {de Kraker, Leander and Seignette, Koen and Thamizharasu, Premnath and van den Boom, Bastijn J.G. and Ferreira Pica, Ildefonso and Willuhn, Ingo and Levelt, Christiaan N. and Togt, Chris van der},
+ doi = {10.1016/j.crmeth.2022.100299},
+ issn = {2667-2375},
+ journal = {Cell Reports Methods},
+ keywords = {Calcium Imaging, Two-Photon},
+ month = {October},
+ number = {10},
+ pages = {100299},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {SpecSeg is a versatile toolbox that segments neurons and neurites in chronic calcium imaging datasets based on low-frequency cross-spectral power},
+ url = {http://dx.doi.org/10.1016/j.crmeth.2022.100299},
+ volume = {2},
+ year = {2022}
+}
+
+@article{larosa_2024_social,
+ author = {Larosa, Amanda and Xu, Qi Wei and Wong, Alice S. and Lee, J. Quinn and Brandon, Mark P. and Wong, Tak Pan},
+ doi = {10.1101/2024.06.07.598039},
+ month = {June},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Social valence dictates sex differences in identity recognition},
+ url = {http://dx.doi.org/10.1101/2024.06.07.598039},
+ year = {2024}
+}
+
+@article{lee_2023_identifying,
+ author = {Lee, J. Quinn and Keinath, Alexandra T. and Cianfarano, Erica and Brandon, Mark P.},
+ doi = {10.1101/2023.10.08.561112},
+ month = {October},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Identifying representational structure in CA1 to benchmark theoretical models of cognitive mapping},
+ url = {http://dx.doi.org/10.1101/2023.10.08.561112},
+ year = {2023}
+}
+
+@article{leman_2021_largescale,
+ author = {Leman, D.P. and Chen, I.A. and Bolding, K.A. and Tai, J. and Wilmerding, L.K. and Gritton, H.J. and Cohen, Y. and Yen, W.W. and Perkins, L.N. and Liberti, W.A. and Kilic, K. and Han, X. and Cruz-Martín, A. and Gardner, T.J. and Otchy, T.M. and Davison, I.G.},
+ doi = {10.1101/2021.01.15.426462},
+ month = {January},
+ project = {Miniscope DAQ},
+ publisher = {openRxiv},
+ title = {Large-scale cellular-resolution imaging of neural activity in freely behaving mice},
+ url = {http://dx.doi.org/10.1101/2021.01.15.426462},
+ year = {2021}
+}
+
+@article{levy_2023_manifold,
+ author = {Levy, Eliott Robert Joseph and Carrillo-Segura, Simón and Park, Eun Hye and Redman, William Thomas and Hurtado, José Rafael and Chung, SueYeon and Fenton, André Antonio},
+ doi = {10.1016/j.celrep.2023.113142},
+ issn = {2211-1247},
+ journal = {Cell Reports},
+ keywords = {Hippocampus, Place Cells, Spatial Navigation, Calcium Imaging},
+ month = {October},
+ number = {10},
+ pages = {113142},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {A manifold neural population code for space in hippocampal coactivity dynamics independent of place fields},
+ url = {http://dx.doi.org/10.1016/j.celrep.2023.113142},
+ volume = {42},
+ year = {2023}
+}
+
+@article{li_2022_opensource,
+ author = {Li, Mingkang and Liu, Changhao and Cui, Xin and Jung, Hayoung and You, Heecheon and Feng, Linqing and Zhang, Shaomin},
+ doi = {10.3389/fncir.2022.891825},
+ issn = {1662-5110},
+ journal = {Frontiers in Neural Circuits},
+ keywords = {Open-Source},
+ month = {June},
+ project = {Miniscope V3},
+ publisher = {Frontiers Media SA},
+ title = {An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy},
+ url = {http://dx.doi.org/10.3389/fncir.2022.891825},
+ volume = {16},
+ year = {2022}
+}
+
+@article{li_2024_cholecystokinin,
+ author = {Li, Hao and Feng, Jingyu and Chen, Mengying and Xin, Min and Chen, Xi and Liu, Wenhao and Wang, Liping and Wang, Kuan Hong and He, Jufang},
+ doi = {10.7554/elife.83897},
+ issn = {2050-084X},
+ journal = {eLife},
+ month = {May},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {Cholecystokinin facilitates motor skill learning by modulating neuroplasticity in the motor cortex},
+ url = {http://dx.doi.org/10.7554/elife.83897},
+ volume = {13},
+ year = {2024}
+}
+
+@article{li_2024_stable,
+ author = {Li, Yiting and Yin, Wenqu and Wang, Xin and Li, Jiawen and Zhou, Shanglin and Ma, Chaolin and Yuan, Peng and Li, Baoming},
+ doi = {10.1101/2024.02.26.582071},
+ month = {February},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Stable sequential dynamics in prefrontal cortex represents subjective estimation of time},
+ url = {http://dx.doi.org/10.1101/2024.02.26.582071},
+ year = {2024}
+}
+
+@article{liao_2024_dualmode,
+ author = {Liao, Yuheng and Qin, Chunlian and Zhang, Xiaoyu and Ye, Jing and Xu, Zhongyuan and Zong, Haotian and Hu, Ning and Zhang, Diming},
+ doi = {10.1016/j.talanta.2024.126537},
+ issn = {0039-9140},
+ journal = {Talanta},
+ month = {October},
+ pages = {126537},
+ project = {Miniscope V4},
+ publisher = {Elsevier BV},
+ title = {A dual-mode, image-enhanced, miniaturized microscopy system for incubator-compatible monitoring of live cells},
+ url = {http://dx.doi.org/10.1016/j.talanta.2024.126537},
+ volume = {278},
+ year = {2024}
+}
+
+@article{lin_2022_spatial,
+ author = {Lin, Xiaoxiao and Chen, Lujia and Baglietto-Vargas, David and Kamalipour, Parsa and Ye, Qiao and LaFerla, Frank M. and Nitz, Douglas A. and Holmes, Todd C. and Xu, Xiangmin},
+ doi = {10.1016/j.nbd.2021.105562},
+ issn = {0969-9961},
+ journal = {Neurobiology of Disease},
+ keywords = {Calcium Imaging, Aging},
+ month = {January},
+ pages = {105562},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Spatial coding defects of hippocampal neural ensemble calcium activities in the triple-transgenic Alzheimer’s disease mouse model},
+ url = {http://dx.doi.org/10.1016/j.nbd.2021.105562},
+ volume = {162},
+ year = {2022}
+}
+
+@article{lin_2022_longitudinal,
+ author = {Lin, Xiaoxiao and Chen, Lujia and Jullienne, Amandine and Zhang, Hai and Salehi, Arjang and Hamer, Mary and C. Holmes, Todd and Obenaus, Andre and Xu, Xiangmin},
+ doi = {10.1186/s40478-022-01361-4},
+ issn = {2051-5960},
+ journal = {Acta Neuropathologica Communications},
+ month = {April},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Longitudinal dynamics of microvascular recovery after acquired cortical injury},
+ url = {http://dx.doi.org/10.1186/s40478-022-01361-4},
+ volume = {10},
+ year = {2022}
+}
+
+@article{lin_2024_hippocampal,
+ author = {Lin, Huixin and Zhou, Jingfeng},
+ doi = {10.1038/s41467-024-49652-9},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Hippocampus, Reward},
+ month = {June},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Hippocampal and orbitofrontal neurons contribute to complementary aspects of associative structure},
+ url = {http://dx.doi.org/10.1038/s41467-024-49652-9},
+ volume = {15},
+ year = {2024}
+}
+
+@article{long_2024_constraints,
+ author = {Long, Charltien and Lee, Kwang and Yang, Long and Dafalias, Theresia and Wu, Alexander K. and Masmanidis, Sotiris C.},
+ doi = {10.1038/s41593-024-01699-z},
+ issn = {1546-1726},
+ journal = {Nature Neuroscience},
+ keywords = {Reward, Neural Circuits},
+ month = {July},
+ number = {10},
+ pages = {1977–1986},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Constraints on the subsecond modulation of striatal dynamics by physiological dopamine signaling},
+ url = {http://dx.doi.org/10.1038/s41593-024-01699-z},
+ volume = {27},
+ year = {2024}
+}
+
+@article{malvaut_2020_deciphering,
+ author = {Malvaut, Sarah and Constantinescu, Vlad-Stefan and Dehez, Harold and Doric, Sead and Saghatelyan, Armen},
+ doi = {10.3389/fnins.2020.00819},
+ issn = {1662-453X},
+ journal = {Frontiers in Neuroscience},
+ keywords = {Calcium Imaging, Freely-Behaving, Open-Source},
+ month = {August},
+ paper_type = {Review},
+ publisher = {Frontiers Media SA},
+ title = {Deciphering Brain Function by Miniaturized Fluorescence Microscopy in Freely Behaving Animals},
+ url = {http://dx.doi.org/10.3389/fnins.2020.00819},
+ volume = {14},
+ year = {2020}
+}
+
+@article{manno_2022_environmental,
+ author = {Manno, Francis A.M. and An, Ziqi and Kumar, Rachit and Su, Junfeng and Liu, Jiaming and Wu, Ed X. and He, Jufang and Feng, Yanqiu and Lau, Condon},
+ doi = {10.1016/j.neuroimage.2022.119016},
+ issn = {1053-8119},
+ journal = {NeuroImage},
+ month = {May},
+ pages = {119016},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Environmental enrichment leads to behavioral circadian shifts enhancing brain-wide functional connectivity between sensory cortices and eliciting increased hippocampal spiking},
+ url = {http://dx.doi.org/10.1016/j.neuroimage.2022.119016},
+ volume = {252},
+ year = {2022}
+}
+
+@article{mau_2022_ensemble,
+ author = {Mau, William and Baggetta, Austin M. and Dong, Zhe and Sweis, Brian M. and Morales-Rodriguez, Denisse and Pennington, Zachary T. and Francisco, Taylor and Freedman, David J. and Baxter, Mark G. and Shuman, Tristan and Cai, Denise J.},
+ doi = {10.1101/2022.06.02.494530},
+ month = {June},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Ensemble remodeling supports memory-updating},
+ url = {http://dx.doi.org/10.1101/2022.06.02.494530},
+ year = {2022}
+}
+
+@article{mills_2022_amygdalostriatal,
+ author = {Mills, Fergil and Lee, Christopher R. and Howe, James R. and Li, Hao and Shao, Shan and Keisler, Maria N. and Lemieux, Mackenzie E. and Taschbach, Felix H. and Keyes, Laurel R. and Borio, Matilde and Chen, Hannah S. and Patel, Reesha R. and Gross, Alexa L. and Delahanty, Jeremy and Cazares, Christian and Maree, Liezl and Wichmann, Romy and Pereira, Talmo D. and Benna, Marcus K. and Root, Cory M. and Tye, Kay M.},
+ doi = {10.1101/2022.10.28.514263},
+ month = {October},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors},
+ url = {http://dx.doi.org/10.1101/2022.10.28.514263},
+ year = {2022}
+}
+
+@article{mishchanchuk_2024_hidden,
+ author = {Mishchanchuk, Karyna and Gregoriou, Gabrielle and Qü, Albert and Kastler, Alizée and Huys, Quentin and Wilbrecht, Linda and MacAskill, Andrew F.},
+ doi = {10.1101/2024.05.17.594673},
+ month = {May},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Hidden state inference requires abstract contextual representations in ventral hippocampus},
+ url = {http://dx.doi.org/10.1101/2024.05.17.594673},
+ year = {2024}
+}
+
+@article{mosser_2020_scpmcgillmouseminiscopescp,
+ author = {Mosser, Coralie‐Anne and Haqqee, Zeeshan and Nieto‐Posadas, Andrés and Murai, Keith K. and Stifani, Stefano and Williams, Sylvain and Brandon, Mark P.},
+ doi = {10.1111/gbb.12686},
+ issn = {1601-183X},
+ journal = {Genes, Brain and Behavior},
+ keywords = {Calcium Imaging},
+ month = {August},
+ number = {1},
+ project = {Miniscope V3},
+ publisher = {Wiley},
+ title = {The
+McGill‐Mouse‐Miniscope
+platform: A standardized approach for high‐throughput imaging of neuronal dynamics during behavior},
+ url = {http://dx.doi.org/10.1111/gbb.12686},
+ volume = {20},
+ year = {2020}
+}
+
+@article{newman_2023_unified,
+ author = {Newman, Jonathan P. and Zhang, Jie and Cuevas-López, Aarón and Miller, Nicholas J. and Honda, Takato and van der Goes, Marie-Sophie H. and Leighton, Alexandra H. and Carvalho, Filipe and Lopes, Gonçalo and Lakunina, Anna and Siegle, Joshua H. and Harnett, Mark T. and Wilson, Matthew A. and Voigts, Jakob},
+ doi = {10.1101/2023.08.30.554672},
+ month = {September},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior},
+ url = {http://dx.doi.org/10.1101/2023.08.30.554672},
+ year = {2023}
+}
+
+@article{nogueira_2020_loud,
+ author = {Nogueira, Ingrid and Winne, Jessica and Lima, Thiago Z. and Malfatti, Thawann and Leao, Richardson N. and Leao, Katarina E.},
+ doi = {10.1101/2020.08.25.264200},
+ month = {August},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Loud noise exposure differentially affects subpopulations of auditory cortex pyramidal cells},
+ url = {http://dx.doi.org/10.1101/2020.08.25.264200},
+ year = {2020}
+}
+
+@article{oh_2019_imaging,
+ author = {Oh, Jihae and Lee, Chiwoo and Kaang, Bong-Kiun},
+ doi = {10.4196/kjpp.2019.23.4.237},
+ issn = {2093-3827},
+ journal = {The Korean Journal of Physiology & Pharmacology},
+ number = {4},
+ pages = {237},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {The Korean Physiological Society and The Korean Society of Pharmacology},
+ title = {Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors},
+ url = {http://dx.doi.org/10.4196/kjpp.2019.23.4.237},
+ volume = {23},
+ year = {2019}
+}
+
+@inbook{ohkawa_2022_miniature,
+ author = {Ohkawa, Noriaki and Ghandour, Khaled},
+ booktitle = {Behavioral Neurogenetics},
+ doi = {10.1007/978-1-0716-2321-3_10},
+ isbn = {9781071623213},
+ issn = {1940-6045},
+ pages = {157–174},
+ paper_type = {Protocol},
+ project = {Miniscope V3},
+ publisher = {Springer US},
+ title = {Miniature Microscopy of Hippocampal CA1 to Identify Engram Cells and Record Calcium Transients for Analyses of Ensemble Activities},
+ url = {http://dx.doi.org/10.1007/978-1-0716-2321-3_10},
+ year = {2022}
+}
+
+@article{petter_2023_elucidating,
+ author = {Petter, Elijah A and Fallon, Isabella P and Hughes, Ryan N and Watson, Glenn DR and Meck, Warren H and Ulloa Severino, Francesco Paolo and Yin, Henry H},
+ doi = {10.7554/elife.83600},
+ issn = {2050-084X},
+ journal = {eLife},
+ keywords = {Hippocampus, Dopamine, Locus Coeruleus},
+ month = {April},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {Elucidating a locus coeruleus-dentate gyrus dopamine pathway for operant reinforcement},
+ url = {http://dx.doi.org/10.7554/elife.83600},
+ volume = {12},
+ year = {2023}
+}
+
+@article{ramirez_armenta_2021_optogenetic,
+ author = {Ramírez-Armenta, Kathia I. and Alatriste-León, Hector and Verma-Rodríguez, Anil K. and Llanos-Moreno, Argelia and Ramírez-Jarquín, Josué O. and Tecuapetla, Fatuel},
+ doi = {10.1038/s41386-021-01161-9},
+ issn = {1740-634X},
+ journal = {Neuropsychopharmacology},
+ month = {August},
+ number = {2},
+ pages = {477–487},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Optogenetic inhibition of indirect pathway neurons in the dorsomedial striatum reduces excessive grooming in Sapap3-knockout mice},
+ url = {http://dx.doi.org/10.1038/s41386-021-01161-9},
+ volume = {47},
+ year = {2021}
+}
+
+@article{raymond_2024_neural,
+ author = {Raymond, Martin A. and Chapman, Ian F. and Staszko, Stephanie M. and Fletcher, Max L. and Boughter, John D.},
+ doi = {10.1101/2024.02.28.582584},
+ month = {March},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Neural coding in gustatory cortex reflects consumption decisions: Evidence from conditioned taste aversion},
+ url = {http://dx.doi.org/10.1101/2024.02.28.582584},
+ year = {2024}
+}
+
+@article{reis_2021_dorsal,
+ author = {Reis, Fernando MCV and Lee, Johannes Y and Maesta-Pereira, Sandra and Schuette, Peter J and Chakerian, Meghmik and Liu, Jinhan and La-Vu, Mimi Q and Tobias, Brooke C and Ikebara, Juliane M and Kihara, Alexandre Hiroaki and Canteras, Newton S and Kao, Jonathan C and Adhikari, Avishek},
+ doi = {10.7554/elife.64934},
+ issn = {2050-084X},
+ journal = {eLife},
+ keywords = {Calcium Imaging, Fear & Anxiety, Periaqueductal Gray},
+ month = {May},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {Dorsal periaqueductal gray ensembles represent approach and avoidance states},
+ url = {http://dx.doi.org/10.7554/elife.64934},
+ volume = {10},
+ year = {2021}
+}
+
+@article{reis_2021_shared,
+ author = {Reis, Fernando M.C.V. and Liu, Jinhan and Schuette, Peter J. and Lee, Johannes Y. and Maesta-Pereira, Sandra and Chakerian, Meghmik and Wang, Weisheng and Canteras, Newton S. and Kao, Jonathan C. and Adhikari, Avishek},
+ doi = {10.1523/jneurosci.2450-20.2021},
+ issn = {1529-2401},
+ journal = {The Journal of Neuroscience},
+ keywords = {Calcium Imaging, Fear & Anxiety, Periaqueductal Gray},
+ month = {April},
+ number = {25},
+ pages = {5399–5420},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Society for Neuroscience},
+ title = {Shared Dorsal Periaqueductal Gray Activation Patterns during Exposure to Innate and Conditioned Threats},
+ url = {http://dx.doi.org/10.1523/jneurosci.2450-20.2021},
+ volume = {41},
+ year = {2021}
+}
+
+@article{rozeske_2023_representational,
+ author = {Rozeske, Robert R. and Runtz, Léonie and Keinath, Alexandra T. and Sossin, Aaron and Brandon, Mark P.},
+ doi = {10.1101/2023.09.08.556889},
+ month = {September},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Representational similarity supports rapid context retrieval during fear discrimination in ventral hippocampus},
+ url = {http://dx.doi.org/10.1101/2023.09.08.556889},
+ year = {2023}
+}
+
+@article{rynes_2021_miniaturized,
+ author = {Rynes, Mathew L. and Surinach, Daniel A. and Linn, Samantha and Laroque, Michael and Rajendran, Vijay and Dominguez, Judith and Hadjistamoulou, Orestes and Navabi, Zahra S. and Ghanbari, Leila and Johnson, Gregory W. and Nazari, Mojtaba and Mohajerani, Majid H. and Kodandaramaiah, Suhasa B.},
+ doi = {10.1038/s41592-021-01104-8},
+ issn = {1548-7105},
+ journal = {Nature Methods},
+ month = {April},
+ number = {4},
+ pages = {417–425},
+ project = {Miniscope DAQ},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice},
+ url = {http://dx.doi.org/10.1038/s41592-021-01104-8},
+ volume = {18},
+ year = {2021}
+}
+
+@article{schall_2024_temporal,
+ author = {Schall, Terra A. and Li, King-Lun and Qi, Xiguang and Lee, Brian T. and Wright, William J. and Alpaugh, Erin E. and Zhao, Rachel J. and Liu, Jianwei and Li, Qize and Zeng, Bo and Wang, Lirong and Huang, Yanhua H. and Schlüter, Oliver M. and Nestler, Eric J. and Nieh, Edward H. and Dong, Yan},
+ doi = {10.1101/2024.09.27.615291},
+ keywords = {Wire-Free},
+ month = {September},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Temporal Dynamics of Nucleus Accumbens Neurons in Male Mice During Reward Seeking},
+ url = {http://dx.doi.org/10.1101/2024.09.27.615291},
+ year = {2024}
+}
+
+@article{scherrer_2023_optical,
+ author = {Scherrer, Josefa R. and Lynch, Galen F. and Zhang, Jie J. and Fee, Michale S.},
+ doi = {10.1038/s41592-023-01806-1},
+ issn = {1548-7105},
+ journal = {Nature Methods},
+ month = {March},
+ number = {4},
+ pages = {546–549},
+ project = {Miniscope DAQ},
+ publisher = {Springer Science and Business Media LLC},
+ title = {An optical design enabling lightweight and large field-of-view head-mounted microscopes},
+ url = {http://dx.doi.org/10.1038/s41592-023-01806-1},
+ volume = {20},
+ year = {2023}
+}
+
+@article{schuette_2020_longterm,
+ author = {Schuette, Peter J. and Reis, Fernando M. C. V. and Maesta-Pereira, Sandra and Chakerian, Meghmik and Torossian, Anita and Blair, Garrett J. and Wang, Weisheng and Blair, Hugh T. and Fanselow, Michael S. and Kao, Jonathan C. and Adhikari, Avishek},
+ doi = {10.1523/jneurosci.1022-20.2020},
+ issn = {1529-2401},
+ journal = {The Journal of Neuroscience},
+ keywords = {Calcium Imaging, Hippocampus, Place Cells},
+ month = {September},
+ number = {43},
+ pages = {8329–8342},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Society for Neuroscience},
+ title = {Long-Term Characterization of Hippocampal Remapping during Contextual Fear Acquisition and Extinction},
+ url = {http://dx.doi.org/10.1523/jneurosci.1022-20.2020},
+ volume = {40},
+ year = {2020}
+}
+
+@article{schuette_2022_gabaergic,
+ author = {Schuette, Peter J. and Ikebara, Juliane M. and Maesta-Pereira, Sandra and Torossian, Anita and Sethi, Ekayana and Kihara, Alexandre H. and Kao, Jonathan C. and Reis, Fernando M. C. V. and Adhikari, Avishek},
+ doi = {10.1038/s41598-022-13799-6},
+ issn = {2045-2322},
+ journal = {Scientific Reports},
+ keywords = {Hippocampus, Memory},
+ month = {June},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {GABAergic CA1 neurons are more stable following context changes than glutamatergic cells},
+ url = {http://dx.doi.org/10.1038/s41598-022-13799-6},
+ volume = {12},
+ year = {2022}
+}
+
+@article{scott_2018_imaging,
+ author = {Scott, Benjamin B. and Thiberge, Stephan Y. and Guo, Caiying and Tervo, D. Gowanlock R. and Brody, Carlos D. and Karpova, Alla Y. and Tank, David W.},
+ doi = {10.1016/j.neuron.2018.09.050},
+ issn = {0896-6273},
+ journal = {Neuron},
+ month = {December},
+ number = {5},
+ pages = {1045-1058.e5},
+ project = {Miniscope DAQ},
+ publisher = {Elsevier BV},
+ title = {Imaging Cortical Dynamics in GCaMP Transgenic Rats with a Head-Mounted Widefield Macroscope},
+ url = {http://dx.doi.org/10.1016/j.neuron.2018.09.050},
+ volume = {100},
+ year = {2018}
+}
+
+@article{shuman_2020_breakdown,
+ author = {Shuman, Tristan and Aharoni, Daniel and Cai, Denise J. and Lee, Christopher R. and Chavlis, Spyridon and Page-Harley, Lucia and Vetere, Lauren M. and Feng, Yu and Yang, Chen Yi and Mollinedo-Gajate, Irene and Chen, Lingxuan and Pennington, Zachary T. and Taxidis, Jiannis and Flores, Sergio E. and Cheng, Kevin and Javaherian, Milad and Kaba, Christina C. and Rao, Naina and La-Vu, Mimi and Pandi, Ioanna and Shtrahman, Matthew and Bakhurin, Konstantin I. and Masmanidis, Sotiris C. and Khakh, Baljit S. and Poirazi, Panayiota and Silva, Alcino J. and Golshani, Peyman},
+ doi = {10.1038/s41593-019-0559-0},
+ issn = {1546-1726},
+ journal = {Nature Neuroscience},
+ keywords = {Hippocampus},
+ month = {January},
+ number = {2},
+ pages = {229–238},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Breakdown of spatial coding and interneuron synchronization in epileptic mice},
+ url = {http://dx.doi.org/10.1038/s41593-019-0559-0},
+ volume = {23},
+ year = {2020}
+}
+
+@article{silva_2017_miniaturized,
+ author = {Silva, Alcino J},
+ doi = {10.1038/lsa.2017.104},
+ issn = {2047-7538},
+ journal = {Light: Science & Applications},
+ month = {August},
+ number = {8},
+ pages = {e17104–e17104},
+ paper_type = {Review},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Miniaturized two-photon microscope: seeing clearer and deeper into the brain},
+ url = {http://dx.doi.org/10.1038/lsa.2017.104},
+ volume = {6},
+ year = {2017}
+}
+
+@article{pfarr_2018_role,
+ author = {Pfarr, Simone},
+ doi = {10.11588/HEIDOK.00025508},
+ keywords = {570 Life sciences},
+ project = {Miniscope V3},
+ publisher = {Heidelberg University Library},
+ title = {The Role of the Medial Prefrontal Cortex in Reward Seeking: Functional Evidence on Cellular and Molecular Mechanisms underlying Drug and Natural Reward Seeking},
+ url = {http://archiv.ub.uni-heidelberg.de/volltextserver/id/eprint/25508},
+ year = {2018}
+}
+
+@article{skocek_2018_highspeed,
+ author = {Skocek, Oliver and Nöbauer, Tobias and Weilguny, Lukas and Martínez Traub, Francisca and Xia, Chuying Naomi and Molodtsov, Maxim I. and Grama, Abhinav and Yamagata, Masahito and Aharoni, Daniel and Cox, David D. and Golshani, Peyman and Vaziri, Alipasha},
+ doi = {10.1038/s41592-018-0008-0},
+ issn = {1548-7105},
+ journal = {Nature Methods},
+ month = {May},
+ number = {6},
+ pages = {429–432},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {High-speed volumetric imaging of neuronal activity in freely moving rodents},
+ url = {http://dx.doi.org/10.1038/s41592-018-0008-0},
+ volume = {15},
+ year = {2018}
+}
+
+@article{smith_2021_opposing,
+ author = {Smith, Alexander C. W. and Jonkman, Sietse and Difeliceantonio, Alexandra G. and O’Connor, Richard M. and Ghoshal, Soham and Romano, Michael F. and Everitt, Barry J. and Kenny, Paul J.},
+ doi = {10.1038/s41467-021-25460-3},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ month = {August},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Opposing roles for striatonigral and striatopallidal neurons in dorsolateral striatum in consolidating new instrumental actions},
+ url = {http://dx.doi.org/10.1038/s41467-021-25460-3},
+ volume = {12},
+ year = {2021}
+}
+
+@article{simoes_de_souza_2024_miniscope,
+ author = {Simoes de Souza, Fabio M. and Williamson, Ryan and McCullough, Connor and Teel, Alec and Futia, Gregory and Ma, Ming and True, Aaron and Crimaldi, John. P. and Gibson, Emily and Restrepo, Diego},
+ doi = {10.1101/2024.06.12.598681},
+ month = {June},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Miniscope Recording Calcium Signals at Hippocampus of Mice Navigating an Odor Plume},
+ url = {http://dx.doi.org/10.1101/2024.06.12.598681},
+ year = {2024}
+}
+
+@article{srinivasan_2019_miniaturized,
+ author = {Srinivasan, Sakthivel and Hosokawa, Takuma and Vergara, Pablo and Chérasse, Yoan and Naoi, Toshie and Sakurai, Takeshi and Sakaguchi, Masanori},
+ doi = {10.1016/j.bbrc.2019.07.082},
+ issn = {0006-291X},
+ journal = {Biochemical and Biophysical Research Communications},
+ keywords = {Hippocampus, Optogenetics},
+ month = {September},
+ number = {3},
+ pages = {520–524},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Miniaturized microscope with flexible light source input for neuronal imaging and manipulation in freely behaving animals},
+ url = {http://dx.doi.org/10.1016/j.bbrc.2019.07.082},
+ volume = {517},
+ year = {2019}
+}
+
+@article{staszko_2022_impact,
+ author = {Staszko, Stephanie M. and Boughter, John D. and Fletcher, Max L.},
+ doi = {10.1016/j.cub.2022.09.053},
+ issn = {0960-9822},
+ journal = {Current Biology},
+ month = {November},
+ number = {22},
+ pages = {4914-4924.e4},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {The impact of familiarity on cortical taste coding},
+ url = {http://dx.doi.org/10.1016/j.cub.2022.09.053},
+ volume = {32},
+ year = {2022}
+}
+
+@article{sun_2019_ca1projecting,
+ author = {Sun, Yanjun and Jin, Suoqin and Lin, Xiaoxiao and Chen, Lujia and Qiao, Xin and Jiang, Li and Zhou, Pengcheng and Johnston, Kevin G. and Golshani, Peyman and Nie, Qing and Holmes, Todd C. and Nitz, Douglas A. and Xu, Xiangmin},
+ doi = {10.1038/s41593-019-0496-y},
+ issn = {1546-1726},
+ journal = {Nature Neuroscience},
+ keywords = {Hippocampus, Neural Circuits},
+ month = {September},
+ number = {11},
+ pages = {1857–1870},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {CA1-projecting subiculum neurons facilitate object–place learning},
+ url = {http://dx.doi.org/10.1038/s41593-019-0496-y},
+ volume = {22},
+ year = {2019}
+}
+
+@article{sun_2021_neural,
+ author = {Sun, Yanjun and Giocomo, Lisa M},
+ doi = {10.1101/2021.09.02.458796},
+ month = {September},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Neural circuit dynamics of drug-context associative learning in the hippocampus},
+ url = {http://dx.doi.org/10.1101/2021.09.02.458796},
+ year = {2021}
+}
+
+@article{sun_2021_scopolamine,
+ author = {Sun, Dechuan and Unnithan, Ranjith Rajasekharan and French, Chris},
+ doi = {10.3389/fnins.2021.640350},
+ issn = {1662-453X},
+ journal = {Frontiers in Neuroscience},
+ keywords = {Calcium Imaging, Place Cells},
+ month = {March},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Frontiers Media SA},
+ title = {Scopolamine Impairs Spatial Information Recorded With “Miniscope” Calcium Imaging in Hippocampal Place Cells},
+ url = {http://dx.doi.org/10.3389/fnins.2021.640350},
+ volume = {15},
+ year = {2021}
+}
+
+@article{sun_2022_neural,
+ author = {Sun, Yanjun and Giocomo, Lisa M.},
+ doi = {10.1038/s41467-022-34114-x},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {Hippocampus, Neural Circuits},
+ month = {November},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Neural circuit dynamics of drug-context associative learning in the mouse hippocampus},
+ url = {http://dx.doi.org/10.1038/s41467-022-34114-x},
+ volume = {13},
+ year = {2022}
+}
+
+@article{sun_2024_hippocampal,
+ author = {Sun, Dechuan and Shaik, Noor E. Karishma and Unnithan, Ranjith Rajasekharan and French, Chris},
+ doi = {10.1016/j.isci.2023.108603},
+ issn = {2589-0042},
+ journal = {iScience},
+ keywords = {Hippocampus, Calcium Imaging, Memory},
+ month = {January},
+ number = {1},
+ pages = {108603},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Elsevier BV},
+ title = {Hippocampal cognitive and relational map paradigms explored by multisensory encoding recording with wide-field calcium imaging},
+ url = {http://dx.doi.org/10.1016/j.isci.2023.108603},
+ volume = {27},
+ year = {2024}
+}
+
+@article{sun_2023_subiculum,
+ author = {Sun, Yanjun and Nitz, Douglas A and Xu, Xiangmin and Giocomo, Lisa M},
+ doi = {10.1101/2023.05.07.539721},
+ month = {May},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {The subiculum encodes environmental geometry},
+ url = {http://dx.doi.org/10.1101/2023.05.07.539721},
+ year = {2023}
+}
+
+@article{sun_2024_protocol,
+ author = {Sun, Dechuan and Amiri, Mona and Unnithan, Ranjith Rajasekharan and French, Chris},
+ doi = {10.1016/j.xpro.2024.103110},
+ issn = {2666-1667},
+ journal = {STAR Protocols},
+ month = {June},
+ number = {2},
+ pages = {103110},
+ paper_type = {Protocol},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Protocol for calcium imaging and analysis of hippocampal CA1 activity evoked by non-spatial stimuli},
+ url = {http://dx.doi.org/10.1016/j.xpro.2024.103110},
+ volume = {5},
+ year = {2024}
+}
+
+@article{sun_2024_subicular,
+ author = {Sun, Yanjun and Nitz, Douglas A. and Xu, Xiangmin and Giocomo, Lisa M.},
+ doi = {10.1038/s41586-024-07139-z},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Neural Circuits},
+ month = {March},
+ number = {8005},
+ pages = {821–829},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Subicular neurons encode concave and convex geometries},
+ url = {http://dx.doi.org/10.1038/s41586-024-07139-z},
+ volume = {627},
+ year = {2024}
+}
+
+@article{tobias_2023_characterization,
+ author = {Tobias, Brooke C. and Schuette, Peter J. and Maesta‐Pereira, Sandra and Torossian, Anita and Wang, Weisheng and Sethi, Ekayana and Adhikari, Avishek},
+ doi = {10.1111/ejn.15937},
+ issn = {1460-9568},
+ journal = {European Journal of Neuroscience},
+ month = {February},
+ number = {7},
+ pages = {1053–1067},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Wiley},
+ title = {Characterization of ventromedial hypothalamus activity during exposure to innate and conditioned threats},
+ url = {http://dx.doi.org/10.1111/ejn.15937},
+ volume = {57},
+ year = {2023}
+}
+
+@article{vassilev_2022_custombuilt,
+ author = {Vassilev, Philip and Fonseca, Esmeralda and Hernandez, Giovanni and Pantoja-Urban, Andrea Haree and Giroux, Michel and Nouel, Dominique and Van Leer, Elise and Flores, Cecilia},
+ doi = {10.1523/eneuro.0430-21.2022},
+ issn = {2373-2822},
+ journal = {eneuro},
+ keywords = {Calcium Imaging, Open-Source},
+ month = {January},
+ number = {1},
+ pages = {ENEURO.0430-21.2022},
+ project = {Miniscope V3},
+ publisher = {Society for Neuroscience},
+ title = {Custom-Built Operant Conditioning Setup for Calcium Imaging and Cognitive Testing in Freely Moving Mice},
+ url = {http://dx.doi.org/10.1523/eneuro.0430-21.2022},
+ volume = {9},
+ year = {2022}
+}
+
+@article{van_der_veldt_2021_conjunctive,
+ author = {van der Veldt, Suzanne and Etter, Guillaume and Mosser, Coralie-Anne and Manseau, Frédéric and Williams, Sylvain},
+ doi = {10.1371/journal.pbio.3001383},
+ editor = {Csicsvari, Jozsef},
+ issn = {1545-7885},
+ journal = {PLOS Biology},
+ keywords = {Hippocampus},
+ month = {August},
+ number = {8},
+ pages = {e3001383},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Public Library of Science (PLoS)},
+ title = {Conjunctive spatial and self-motion codes are topographically organized in the GABAergic cells of the lateral septum},
+ url = {http://dx.doi.org/10.1371/journal.pbio.3001383},
+ volume = {19},
+ year = {2021}
+}
+
+@article{vergara_2023_caliali,
+ author = {Vergara, Pablo and Wang, Yuteng and Srinivasan, Sakthivel and Cherasse, Yoan and Naoi, Toshie and Sugaya, Yuki and Sakurai, Takeshi and Kano, Masanobu and Sakaguchi, Masanori},
+ doi = {10.1101/2023.05.19.540935},
+ month = {May},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging},
+ url = {http://dx.doi.org/10.1101/2023.05.19.540935},
+ year = {2023}
+}
+
+@article{vogel_2022_prefrontal,
+ author = {Vogel, Pascal and Hahn, Johannes and Duvarci, Sevil and Sigurdsson, Torfi},
+ doi = {10.1016/j.celrep.2022.110659},
+ issn = {2211-1247},
+ journal = {Cell Reports},
+ keywords = {Calcium Imaging, Optogenetics, Prefrontal Cortex, Memory},
+ month = {April},
+ number = {2},
+ pages = {110659},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Prefrontal pyramidal neurons are critical for all phases of working memory},
+ url = {http://dx.doi.org/10.1016/j.celrep.2022.110659},
+ volume = {39},
+ year = {2022}
+}
+
+@article{vu_2024_targeted,
+ author = {Vu, Mai-Anh T. and Brown, Eleanor H. and Wen, Michelle J. and Noggle, Christian A. and Zhang, Zicheng and Monk, Kevin J. and Bouabid, Safa and Mroz, Lydia and Graham, Benjamin M. and Zhuo, Yizhou and Li, Yulong and Otchy, Timothy M. and Tian, Lin and Davison, Ian G. and Boas, David A. and Howe, Mark W.},
+ doi = {10.1016/j.neuron.2023.12.011},
+ issn = {0896-6273},
+ journal = {Neuron},
+ keywords = {Dopamine},
+ month = {March},
+ number = {6},
+ pages = {909–923.e9},
+ project = {Miniscope DAQ},
+ publisher = {Elsevier BV},
+ title = {Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior},
+ url = {http://dx.doi.org/10.1016/j.neuron.2023.12.011},
+ volume = {112},
+ year = {2024}
+}
+
+@article{wang_2021_coordination,
+ author = {Wang, Weisheng and Schuette, Peter J. and Nagai, Jun and Tobias, Brooke Christine and Cuccovia V. Reis, Fernando Midea and Ji, Shiyu and de Lima, Miguel A.X. and La-Vu, Mimi Q. and Maesta-Pereira, Sandra and Chakerian, Meghmik and Leonard, Saskia J. and Lin, Lilly and Severino, Amie L. and Cahill, Catherine M. and Canteras, Newton S. and Khakh, Baljit S. and Kao, Jonathan C. and Adhikari, Avishek},
+ doi = {10.1016/j.neuron.2021.03.033},
+ issn = {0896-6273},
+ journal = {Neuron},
+ keywords = {Calcium Imaging, Optogenetics, Fear & Anxiety},
+ month = {June},
+ number = {11},
+ pages = {1848-1860.e8},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Coordination of escape and spatial navigation circuits orchestrates versatile flight from threats},
+ url = {http://dx.doi.org/10.1016/j.neuron.2021.03.033},
+ volume = {109},
+ year = {2021}
+}
+
+@article{wang_2021_dorsal,
+ author = {Wang, Weisheng and Schuette, Peter J and La-Vu, Mimi Q and Torossian, Anita and Tobias, Brooke C and Ceko, Marta and Kragel, Philip A and Reis, Fernando MCV and Ji, Shiyu and Sehgal, Megha and Maesta-Pereira, Sandra and Chakerian, Meghmik and Silva, Alcino J and Canteras, Newton S and Wager, Tor and Kao, Jonathan C and Adhikari, Avishek},
+ doi = {10.7554/elife.69178},
+ issn = {2050-084X},
+ journal = {eLife},
+ keywords = {Fear & Anxiety, Periaqueductal Gray},
+ month = {September},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {eLife Sciences Publications, Ltd},
+ title = {Dorsal premammillary projection to periaqueductal gray controls escape vigor from innate and conditioned threats},
+ url = {http://dx.doi.org/10.7554/elife.69178},
+ volume = {10},
+ year = {2021}
+}
+
+@article{wang_2022_cablefree,
+ author = {Wang, Yangzhen and Ma, Zhongtian and Li, Wenzhao and Su, Feng and Wang, Chong and Xiong, Wei and Li, Changhui and Zhang, Chen},
+ doi = {10.1101/2022.06.20.496795},
+ month = {June},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Cable-free brain imaging with miniature wireless microscopes},
+ url = {http://dx.doi.org/10.1101/2022.06.20.496795},
+ year = {2022}
+}
+
+@article{wang_2023_somatic,
+ author = {Wang, Ruixue and Han, Jiawei and Hu, Xiaoling and You, Heecheon and Zhang, Shaomin},
+ doi = {10.1101/2023.04.11.536319},
+ month = {April},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Somatic Calcium Signals from Layer II/III Motor Cortex for Continuous Neural Decoding},
+ url = {http://dx.doi.org/10.1101/2023.04.11.536319},
+ year = {2023}
+}
+
+@article{wang_2024_tscope,
+ author = {Wang, Yuteng and Vergara, Pablo and Hasegawa, Satoshi and Tomita, Naoki and Cherasse, Yoan and Naoi, Toshie and Sakurai, Takeshi and Sugaya, Yuki and Kano, Masanobu and Sakaguchi, Masanori},
+ doi = {10.1101/2024.10.07.616920},
+ month = {October},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals},
+ url = {http://dx.doi.org/10.1101/2024.10.07.616920},
+ year = {2024}
+}
+
+@misc{winne_2021_calcium,
+ author = {Winne, Jessica and Nascimento, George and Nogueira, Ingrid and Leao, Richardson N. and Leao, Katarina E.},
+ copyright = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International},
+ doi = {10.48550/ARXIV.2110.00609},
+ keywords = {Neurons and Cognition (q-bio.NC), FOS: Biological sciences, FOS: Biological sciences},
+ paper_type = {Protocol},
+ project = {Miniscope V4},
+ publisher = {arXiv},
+ title = {Calcium imaging and analysis of the mouse hippocampus or neocortex using miniature microendoscopes},
+ url = {https://arxiv.org/abs/2110.00609},
+ year = {2021}
+}
+
+@article{wirtshafter_2022_vivo,
+ author = {Wirtshafter, Hannah S. and Disterhoft, John F.},
+ doi = {10.1523/jneurosci.1750-21.2022},
+ issn = {1529-2401},
+ journal = {The Journal of Neuroscience},
+ keywords = {Calcium Imaging, Hippocampus, Place Cells},
+ month = {May},
+ number = {22},
+ pages = {4538–4554},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Society for Neuroscience},
+ title = {In Vivo
+Multi-Day Calcium Imaging of CA1 Hippocampus in Freely Moving Rats Reveals a High Preponderance of Place Cells with Consistent Place Fields},
+ url = {http://dx.doi.org/10.1523/jneurosci.1750-21.2022},
+ volume = {42},
+ year = {2022}
+}
+
+@article{wirtshafter_2022_place,
+ author = {Wirtshafter, Hannah S. and Disterhoft, John F.},
+ doi = {10.1002/hipo.23489},
+ issn = {1098-1063},
+ journal = {Hippocampus},
+ keywords = {Calcium Imaging, Hippocampus, Reward, Place Cells},
+ month = {December},
+ number = {2},
+ pages = {65–84},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Wiley},
+ title = {Place cells are nonrandomly clustered by field location in CA1 hippocampus},
+ url = {http://dx.doi.org/10.1002/hipo.23489},
+ volume = {33},
+ year = {2022}
+}
+
+@article{wu_2021_modified,
+ author = {Wu, Xiaoting and Yang, Xiangyu and Song, Lulu and Wang, Yang and Li, Yamin and Liu, Yuanyuan and Yang, Xiaowei and Wang, Yijun and Pei, Weihua and Li, Weidong},
+ doi = {10.3389/fnint.2021.682019},
+ issn = {1662-5145},
+ journal = {Frontiers in Integrative Neuroscience},
+ keywords = {Calcium Imaging},
+ month = {August},
+ project = {Miniscope V3},
+ publisher = {Frontiers Media SA},
+ title = {A Modified Miniscope System for Simultaneous Electrophysiology and Calcium Imaging in vivo},
+ url = {http://dx.doi.org/10.3389/fnint.2021.682019},
+ volume = {15},
+ year = {2021}
+}
+
+@article{wu_2021_neural,
+ author = {Wu, Ye Emily and Dang, James and Kingsbury, Lyle and Zhang, Mingmin and Sun, Fangmiao and Hu, Rongfeng K. and Hong, Weizhe},
+ doi = {10.1038/s41586-021-03962-w},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Neural Circuits},
+ month = {October},
+ number = {7884},
+ pages = {262–267},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Neural control of affiliative touch in prosocial interaction},
+ url = {http://dx.doi.org/10.1038/s41586-021-03962-w},
+ volume = {599},
+ year = {2021}
+}
+
+@article{yaghmazadeh_2022_neuronal,
+ author = {Yaghmazadeh, Omid and Vöröslakos, Mihály and Alon, Leeor and Carluccio, Giuseppe and Collins, Christopher and Sodickson, Daniel K. and Buzsáki, György},
+ doi = {10.1038/s44172-022-00014-7},
+ issn = {2731-3395},
+ journal = {Communications Engineering},
+ month = {July},
+ number = {1},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Neuronal activity under transcranial radio-frequency stimulation in metal-free rodent brains in-vivo},
+ url = {http://dx.doi.org/10.1038/s44172-022-00014-7},
+ volume = {1},
+ year = {2022}
+}
+
+@article{yang_2019_twostep,
+ author = {Yang, Yupeng and Zhang, Lifeng and Wang, Zhenni and Liang, Bo and Barbera, Giovanni and Moffitt, Casey and Li, Yun and Lin, Da-Ting},
+ doi = {10.1007/s12264-019-00356-x},
+ issn = {1995-8218},
+ journal = {Neuroscience Bulletin},
+ month = {March},
+ number = {3},
+ pages = {419–424},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {A Two-Step GRIN Lens Coating for In Vivo Brain Imaging},
+ url = {http://dx.doi.org/10.1007/s12264-019-00356-x},
+ volume = {35},
+ year = {2019}
+}
+
+@article{yanny_2020_miniscope3d,
+ author = {Yanny, Kyrollos and Antipa, Nick and Liberti, William and Dehaeck, Sam and Monakhova, Kristina and Liu, Fanglin Linda and Shen, Konlin and Ng, Ren and Waller, Laura},
+ doi = {10.1038/s41377-020-00403-7},
+ issn = {2047-7538},
+ journal = {Light: Science & Applications},
+ month = {October},
+ number = {1},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy},
+ url = {http://dx.doi.org/10.1038/s41377-020-00403-7},
+ volume = {9},
+ year = {2020}
+}
+
+@article{yu_2018_reducing,
+ author = {Yu, Xinzhu and Taylor, Anna M.W. and Nagai, Jun and Golshani, Peyman and Evans, Christopher J. and Coppola, Giovanni and Khakh, Baljit S.},
+ doi = {10.1016/j.neuron.2018.08.015},
+ issn = {0896-6273},
+ journal = {Neuron},
+ month = {September},
+ number = {6},
+ pages = {1170-1187.e9},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Elsevier BV},
+ title = {Reducing Astrocyte Calcium Signaling In Vivo Alters Striatal Microcircuits and Causes Repetitive Behavior},
+ url = {http://dx.doi.org/10.1016/j.neuron.2018.08.015},
+ volume = {99},
+ year = {2018}
+}
+
+@article{zaki_2023_aversive,
+ author = {Zaki, Yosif and Pennington, Zachary T. and Morales-Rodriguez, Denisse and Francisco, Taylor R. and LaBanca, Alexa R. and Dong, Zhe and Lamsifer, Sophia and Segura, Simón Carrillo and Chen, Hung-Tu and Christenson Wick, Zoé and Silva, Alcino J. and van der Meer, Matthijs and Shuman, Tristan and Fenton, André and Rajan, Kanaka and Cai, Denise J.},
+ doi = {10.1101/2023.03.13.532469},
+ month = {March},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Aversive experience drives offline ensemble reactivation to link memories across days},
+ url = {http://dx.doi.org/10.1101/2023.03.13.532469},
+ year = {2023}
+}
+
+@article{zeidler_2020_hippobellum,
+ author = {Zeidler, Zachary and Hoffmann, Katerina and Krook-Magnuson, Esther},
+ doi = {10.1523/jneurosci.0763-20.2020},
+ issn = {1529-2401},
+ journal = {The Journal of Neuroscience},
+ keywords = {Hippocampus, Memory},
+ month = {August},
+ number = {36},
+ pages = {6910–6926},
+ paper_type = {Science},
+ project = {Miniscope V3},
+ publisher = {Society for Neuroscience},
+ title = {HippoBellum: Acute Cerebellar Modulation Alters Hippocampal Dynamics and Function},
+ url = {http://dx.doi.org/10.1523/jneurosci.0763-20.2020},
+ volume = {40},
+ year = {2020}
+}
+
+@article{zhang_2022_onephoton,
+ author = {Zhang, Jinyong and Hughes, Ryan N. and Kim, Namsoo and Fallon, Isabella P. and Bakhurin, Konstantin and Kim, Jiwon and Severino, Francesco Paolo Ulloa and Yin, Henry H.},
+ doi = {10.1038/s41551-022-00920-3},
+ issn = {2157-846X},
+ journal = {Nature Biomedical Engineering},
+ keywords = {Neural Circuits},
+ month = {August},
+ number = {4},
+ pages = {499–510},
+ project = {Miniscope V3},
+ publisher = {Springer Science and Business Media LLC},
+ title = {A one-photon endoscope for simultaneous patterned optogenetic stimulation and calcium imaging in freely behaving mice},
+ url = {http://dx.doi.org/10.1038/s41551-022-00920-3},
+ volume = {7},
+ year = {2022}
+}
+
+@article{zhang_2022_rapid,
+ author = {Zhang, Yuanlong and Zhang, Guoxun and Han, Xiaofei and Wu, Jiamin and Li, Ziwei and Li, Xinyang and Xiao, Guihua and Xie, Hao and Fang, Lu and Dai, Qionghai},
+ doi = {10.1101/2022.01.25.474600},
+ month = {January},
+ project = {Miniscope V3},
+ publisher = {openRxiv},
+ title = {Rapid deep widefield neuron finder driven by virtual calcium imaging data},
+ url = {http://dx.doi.org/10.1101/2022.01.25.474600},
+ year = {2022}
+}
+
+@article{zhang_2023_novel,
+ author = {Zhang, Jinyong and Xin, Xuegang},
+ doi = {10.1109/jphot.2023.3306806},
+ issn = {1943-0647},
+ journal = {IEEE Photonics Journal},
+ keywords = {Calcium Imaging},
+ month = {October},
+ number = {5},
+ pages = {1–6},
+ project = {Miniscope V3},
+ publisher = {Institute of Electrical and Electronics Engineers (IEEE)},
+ title = {A Novel Design Method of Uniformity Energy Distribution Lens for Miniscopes},
+ url = {http://dx.doi.org/10.1109/jphot.2023.3306806},
+ volume = {15},
+ year = {2023}
+}
+
+@article{zhang_2024_cortical,
+ author = {Zhang, Mingmin and Wu, Ye Emily and Jiang, Mengping and Hong, Weizhe},
+ doi = {10.1038/s41586-023-06973-x},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {Neural Circuits},
+ month = {January},
+ number = {7997},
+ pages = {136–144},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {Springer Science and Business Media LLC},
+ title = {Cortical regulation of helping behaviour towards others in pain},
+ url = {http://dx.doi.org/10.1038/s41586-023-06973-x},
+ volume = {626},
+ year = {2024}
+}
+
+@article{zhao_2023_accelerated,
+ author = {Zhao, Pingping and Chen, Xing and Bellafard, Arash and Murugesan, Avaneesh and Quan, Jonathan and Aharoni, Daniel and Golshani, Peyman},
+ doi = {10.1101/2023.08.05.552133},
+ keywords = {Reward, Social Behavior, Calcium Imaging, Optogenetics},
+ month = {August},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Accelerated social representational drift in the nucleus accumbens in a model of autism},
+ url = {http://dx.doi.org/10.1101/2023.08.05.552133},
+ year = {2023}
+}
+
+@article{zhao_2024_minixl,
+ author = {Zhao, Pingping and Guo, Changliang and Xie, Mian and Chen, Liangyi and Golshani, Peyman and Aharoni, Daniel},
+ doi = {10.1101/2024.08.16.608328},
+ month = {August},
+ project = {MiniXL},
+ publisher = {openRxiv},
+ title = {MiniXL: An open-source, large field-of-view epifluorescence miniature microscope for mice capable of single-cell resolution and multi-brain region imaging},
+ url = {http://dx.doi.org/10.1101/2024.08.16.608328},
+ year = {2024}
+}
+
+@article{zhou_2023_conjunctive,
+ author = {Zhou, Yue-Qing and Puliyadi, Vyash and Chen, Xiaojing and Lee, Joonhee Leo and Zhang, Lan-Yuan and Knierim, James J.},
+ doi = {10.1101/2023.06.02.543340},
+ month = {June},
+ paper_type = {Science},
+ project = {Miniscope V4},
+ publisher = {openRxiv},
+ title = {Conjunctive vector coding and place coding in hippocampus share a common directional signal},
+ url = {http://dx.doi.org/10.1101/2023.06.02.543340},
+ year = {2023}
+}
+
+@inproceedings{zhu_2023_multifunctional,
+ author = {Zhu, Xinyi and Gu, Liangtao and Li, Rui and Chen, Liang and Chen, Jingying and Zhou, Ning and Ren, Wuwei},
+ booktitle = {Second Conference on Biomedical Photonics and Cross-Fusion (BPC 2023)},
+ doi = {10.1117/12.2691914},
+ editor = {Qu, Junle and Zhang, Zhenxi and Li, Buhong},
+ month = {July},
+ pages = {24},
+ project = {Miniscope V3},
+ publisher = {SPIE},
+ title = {Multi-functional accessory toolkit for Miniscope prototyping and image enhancement},
+ url = {http://dx.doi.org/10.1117/12.2691914},
+ year = {2023}
+}
+
+@article{zhu_2023_scpminimounterscp,
+ author = {Zhu, Xinyi and Gu, Liangtao and Li, Rui and Chen, Liang and Chen, Jingying and Zhou, Ning and Ren, Wuwei},
+ doi = {10.1002/jbio.202300214},
+ issn = {1864-0648},
+ journal = {Journal of Biophotonics},
+ month = {November},
+ number = {2},
+ project = {Miniscope V3},
+ publisher = {Wiley},
+ title = {MiniMounter: A low‐cost miniaturized microscopy development toolkit for image quality control and enhancement},
+ url = {http://dx.doi.org/10.1002/jbio.202300214},
+ volume = {17},
+ year = {2023}
+}
+
+@mastersthesis{yan_2018_implementing,
+ author = {Yan, Helena Z. H.},
+ keywords = {Calcium Imaging, Optogenetics, Place Cells, Hippocampus, Open-Source},
+ month = {May},
+ paper_type = {Methods},
+ project = {Miniscope V3, Miniscope DAQ},
+ school = {Wellesley College},
+ title = {Implementing simultaneous calcium imaging and optogenetics in freely moving rodents to investigate the role of local inhibition in place field stability},
+ url = {https://repository.wellesley.edu/thesiscollection/574},
+ year = {2018}
+}