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references.bib
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@misc{Zhou2017code,
title = {CNMF-E},
author = {Zhou, Pengcheng},
URL = {https://github.com/zhoupc/CNMF_E},
publisher = {Github},
year = {2017},
note ={088afc1}
}
@misc{Zhou2017scripts,
title = {eLife\_submission},
author = {Zhou, Pengcheng},
URL = {https://github.com/zhoupc/eLife_submission},
publisher = {Github},
year = {2017},
note ={1c65f70}
}
@misc{giovannucci2017code,
title={CaImAn},
author={Giovannucci, Andrea and Friedrich, Johannes and Deverett, Ben and Staneva, Valentina and Chklovskii, Dmitri and Pnevmatikakis, Eftychios A},
URL = {https://github.com/flatironinstitute/CaImAn},
publisher = {Github},
year = {2017},
note ={6bd51e2}
}
@misc{Mukamel2016code,
title={CellSort},
author={Mukamel, Eran A},
URL = {https://github.com/mukamel-lab/CellSort},
publisher = {Github},
year = {2016},
note ={45f28d7}
}
@misc{Pnevmatikakis2016code,
title={ca\_source\_extraction},
author={Pnevmatikakis, Eftychios A},
URL = {https://github.com/epnev/ca_source_extraction},
publisher = {Github},
year = {2016},
note ={5a25d5a}
}
@misc{Zhou2017data,
title = {Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data},
author = {Zhou, Pengcheng and Resendez, Shanna L. and Rodriguez-Romaguera, Jose and Jimenez, Jessica C. and Neufeld, Shay Q. and Giovannucci, Andrea and Friedrich, Johannes and Pnevmatikakis, Eftychios E and Stuber, Garret D. and Hen, Rene and Kheirbek, Mazen A. and Sabatini, Bernardo L. and Kass, Robert E. and Paninski, Liam},
journal = {eLife},
URL = {https://doi.org/10.5061/dryad.kr17k},
doi = {doi:10.5061/dryad.kr17k},
publisher = {Dryad Digital Repository},
year = {2017}
}
@article{Roberts2017,
title={Identification of a motor-to-auditory pathway important for vocal learning},
author={Roberts, Todd F and Hisey, Erin and Tanaka, Masashi and Kearney, Matthew G and Chattree, Gaurav and Yang, Cindy F and Shah, Nirao M and Mooney, Richard},
journal={Nature Neuroscience},
year={2017},
publisher={Nature Research}
}@article{Ryan2017,
title={Oxytocin-receptor-expressing neurons in the parabrachial nucleus regulate fluid intake},
author={Ryan, Philip J and Ross, Silvano I and Campos, Carlos A and Derkach, Victor A and Palmiter, Richard D},
journal={Nature Neuroscience},
pages={1},
year={2017},
publisher={Nature Publishing Group}
}
@article{Mohammed2016,
title={An integrative approach for analyzing hundreds of neurons in task performing mice using wide-field calcium imaging},
author={Mohammed, Ali I and Gritton, Howard J and Tseng, Hua-an and Bucklin, Mark E and Yao, Zhaojie and Han, Xue},
journal={Scientific reports},
volume={6},
year={2016},
publisher={Nature Publishing Group}
}
@article{sheintuch2017tracking,
title={Tracking the Same Neurons across Multiple Days in Ca2+ Imaging Data},
author={Sheintuch, Liron and Rubin, Alon and Brande-Eilat, Noa and Geva, Nitzan and Sadeh, Noa and Pinchasof, Or and Ziv, Yaniv},
journal={Cell Reports},
volume={21},
number={4},
pages={1102},
year={2017},
publisher={Elsevier}
}
@article{giovannucci2017,
title={CaImAn: An open source toolbox for large scale calcium imaging data analysis on standalone machines},
author={Giovannucci, Andrea and Friedrich, Johannes and Deverett, Ben and Staneva, Valentina and Chklovskii, Dmitri and Pnevmatikakis, Eftychios A},
journal={Cosyne Abstracts},
year={2017}
}
@article{Sheintuch2017,
annote = {doi: 10.1016/j.celrep.2017.10.013},
author = {Sheintuch, Liron and Rubin, Alon and Brande-Eilat, Noa and Geva, Nitzan and Sadeh, Noa and Pinchasof, Or and Ziv, Yaniv},
doi = {10.1016/j.celrep.2017.10.013},
issn = {2211-1247},
journal = {Cell Reports},
month = {oct},
number = {4},
pages = {1102--1115},
publisher = {Elsevier},
title = {{Tracking the Same Neurons across Multiple Days in Ca{\textless}sup{\textgreater}2+{\textless}/sup{\textgreater} Imaging Data}},
url = {http://dx.doi.org/10.1016/j.celrep.2017.10.013},
volume = {21},
year = {2017}
}
@article{Roberts2017,
author = {Roberts, Todd F and Hisey, Erin and Tanaka, Masashi and Kearney, Matthew G and Chattree, Gaurav and Yang, Cindy F and Shah, Nirao M and Mooney, Richard},
doi = {10.1038/nn.4563},
file = {:Users/zhoupc/OneDrive/Mendeley/Roberts et al/2017/Nature Neuroscience/Roberts et al. - 2017 - Identification of a motor-to-auditory pathway important for vocal learning.pdf:pdf},
issn = {1097-6256},
journal = {Nature Neuroscience},
number = {April},
publisher = {Nature Publishing Group},
title = {{Identification of a motor-to-auditory pathway important for vocal learning}},
url = {http://www.nature.com/doifinder/10.1038/nn.4563},
year = {2017}
}
@article{Efron2004,
title={Least angle regression},
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year={2004},
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journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{In vivo calcium imaging to assess the role of prelimbic cortex neuronal ensembles in encoding reinstatement of palatable food-seeking in rats.}},
volume = {Poster},
year = {2017}
}
@article{Mackevicius2017,
author = {Mackevicius, Emily M. and Denisenko, Natasha and Fee, Michale. S. ;},
journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{Neural sequences underlying the rapid learning of new syllables in juvenile zebra finches.}},
volume = {Poster},
year = {2017}
}
@article{Cameron2016,
author = {Cameron, C. M. and Pillow, J. and Witten, I. B. },
journal = {2016 Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience},
pages = {259.08 / GGG2},
title = {{Cellular resolution calcium imaging and optogenetic excitation reveal a role for IL to NAc projection neurons in encoding of spatial information during cocaine-seeking.}},
volume = {Poster},
year = {2016}
}
@article{Tombaz2016,
author = {Tombaz, T. and Dunn, B. A. and Hovde, K. and Whitlock J. R. },
journal = {2016 Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience},
pages = {247.06 / SS14 },
title = {{Action planning and action observation in rodent parietal cortex.}},
volume = {Poster},
year = {2016}
}
@article{Ung2017,
author = {Ung, Randall L and Rodriguez-Romaguera, Jose and Nomura, Hiroshi and Namboodiri, Vijay Mohan K and Otis, James M and Robinson, J. Elliott and Resendez, Shanna L and McHenry, Jenna A and Eckman, Louisa E. H. and Kosyk, Thomas L and van den Munkhof, Hanna E. and Zhou, Pengcheng and Paninski, Liam and Kash, Thomas L. and Bruchas, Michael R. and Stuber, Garret D},
journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{Encoding the relationship between anxiety-related behaviors and nociceptin neurons of the bed nucleus of the stria terminalis.}},
volume = {Poster},
year = {2017}
}
@article{Rodriguez-Romaguera2017,
author = {Rodriguez-Romaguera, Jose and Ung, Randall L and Nomura, Hiroshi and Namboodiri, Vijay Mohan K and Otis, James M and Robinson, J. Elliott and Resendez, Shanna L and McHenry, Jenna A and Eckman, Louisa E. H. and Kosyk, Thomas L and van den Munkhof, Hanna E. and Zhou, Pengcheng and Paninski, Liam and Kash, Thomas L. and Bruchas, Michael R. and Stuber, Garret D},
journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{Nociceptin neurons in the bed nucleus of the stria terminalis regulate anxiety.}},
volume = {Poster},
year = {2017}
}
@article{Donahue2017,
author = {Donahue, Christopher H and Kreitzer, Anatol C},
journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{Function of Basal Ganglia Circuitry in Motivation.}},
volume = {Poster},
year = {2017}
}
@article{Lin2017,
author = {Lin, Xiaoxiao and Grieco, Steven F. and Jin, Suoqin and Zhou, Pengcheng and Nie, Qing and Kwapis, Janine and Wood, Marcelo A. and Baglietto-Vargas, David and Laferla, Frank M. and Xu, Xiangmin},
journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{In vivo calcium imaging of hippocampal neuronal network activity associated with memory behavior deficits in the Alzheimer's disease mouse model.}},
volume = {Poster},
year = {2017}
}
@article{Jimenez2017,
author = {Jimenez, J. C. and Su, K. and Goldberg, A. and Luna, V. M. and Zhou, Pengcheng and Ordek, G. and Ong, S and Zweifel, L. and Paninski, Liam and Hen, R. and Kheirbek, M. },
journal = {2017 Neuroscience Meeting Planner. Washinton, DC: Society for Neuroscience},
title = {{Anxiety cells in a hippocampalhypothalamic circuit.}},
volume = {Poster},
year = {2017}
}
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author = {Jimenez, J. C. and Goldberg, A. and Ordek, G. and Luna, V. M. and Su, K. and Pena, S. and Zweifel, L. and Hen, R. and Kheirbek, M. },
journal = {2016 Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience},
pages = {455.10 / JJJ26 },
title = {{Subcortical projection-specific control of innate anxiety and learned fear by the ventral hippocampus.}},
volume = {Poster},
year = {2016}
}
@article{Murugan2017,
title={Combined social and spatial coding in a descending projection from the prefrontal cortex},
author={Murugan, Malavika and Park, Michelle and Taliaferro, Josh and Jang, Hee Jae and Cox, Julia and Parker, Nathan and Bhave, Varun and Nectow, Alexander and Pillow, Jonathan and Witten, Ilana},
journal={bioRxiv},
pages={155929},
year={2017},
publisher={Cold Spring Harbor Laboratory}
}
@article{Murugan2016,
author = {Murugan, M. and Taliaferro, J. P. and Park, M. and Jang, H. and Witten, I. B. },
journal = {2016 Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience},
pages = {260.11/GGG26 },
title = {{Detecting action potentials in neuronal populations with calcium imaging.}},
volume = {Poster},
year = {2016}
}
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author = {Smetters, Diana and Majewska, Ania and Yuste, Rafael},
doi = {10.1006/meth.1999.0774},
isbn = {1046-2023 (Print)},
issn = {1046-2023},
journal = {Methods (San Diego, Calif.)},
keywords = {after,cortex,current understanding of the,multiunit,networks,of certain circuits,processing of informa-,reconstruction of the function,slices,system is based on,the piecemeal,tion in the nervous},
pages = {215--221},
pmid = {10356353},
title = {{Detecting action potentials in neuronal populations with calcium imaging.}},
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year = {1999}
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author = {Cichocki, Andrzej and Phan, Anh Huy},
doi = {10.1587/transfun.E92.A.708},
issn = {09168508},
journal = {IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences},
keywords = {Alpha and beta divergences,Compression,Denoising,Feature extraction,Model reduction,Multiplicative local learning (adaptive) algorithms,Nonnegative PARAFAC,Nonnegative matrix factorization (NMF),Nonnegative tensor factorizations (NTF)},
number = {3},
pages = {708--721},
pmid = {1000253585},
title = {{Fast local algorithms for large scale nonnegative matrix and tensor factorizations}},
volume = {E92-A},
year = {2009}
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author = {Dombeck, Daniel A and Graziano, Michael S and Tank, David W},
doi = {10.1523/JNEUROSCI.2985-09.2009},
isbn = {1529-2401 (Electronic)$\backslash$r0270-6474 (Linking)},
issn = {1529-2401},
journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
keywords = {Animals,Cluster Analysis,Computer-Assisted,Computer-Assisted: methods,Diagnostic Imaging,Diagnostic Imaging: methods,Fluorescence,Image Processing,Inbred CBA,Male,Mice,Microscopy,Motor Activity,Motor Activity: physiology,Motor Cortex,Motor Cortex: cytology,Motor Cortex: physiology,Multiphoton,Multiphoton: methods,Neurons,Neurons: cytology,Neurons: physiology,Wakefulness,Wakefulness: physiology},
number = {44},
pages = {13751--60},
pmid = {19889987},
title = {{Functional clustering of neurons in motor cortex determined by cellular resolution imaging in awake behaving mice.}},
volume = {29},
year = {2009}
}
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archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Warp, Erica and Agarwal, Gautam and Wyart, Claire and Friedmann, Drew and Oldfield, Claire S. and Conner, Alden and {Del Bene}, Filippo and Arrenberg, Aristides B. and Baier, Herwig and Isacoff, Ehud Y.},
doi = {10.1016/j.cub.2011.12.002},
eprint = {NIHMS150003},
isbn = {1879-0445 (Electronic)$\backslash$r0960-9822 (Linking)},
issn = {09609822},
journal = {Current Biology},
number = {2},
pages = {93--102},
pmid = {22197243},
title = {{Emergence of patterned activity in the developing zebrafish spinal cord}},
volume = {22},
year = {2012}
}
@article{Klaus2017,
title={The spatiotemporal organization of the striatum encodes action space},
author={Klaus, Andreas and Martins, Gabriela J and Paixao, Vitor B and Zhou, Pengcheng and Paninski, Liam and Costa, Rui M},
journal={Neuron},
volume={95},
number={5},
pages={1171},
year={2017},
publisher={Elsevier}
}
@article{kitamura2017engrams,
title={Engrams and circuits crucial for systems consolidation of a memory},
author={Kitamura, Takashi and Ogawa, Sachie K and Roy, Dheeraj S and Okuyama, Teruhiro and Morrissey, Mark D and Smith, Lillian M and Redondo, Roger L and Tonegawa, Susumu},
journal={Science},
volume={356},
number={6333},
pages={73--78},
year={2017},
publisher={American Association for the Advancement of Science}
}
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author = {Jennings, Joshua H and Sparta, Dennis R and Stamatakis, Alice M and Ung, Randall L and Pleil, Kristen E and Kash, Thomas L and Stuber, Garret D},
doi = {10.1038/nature12041},
eprint = {NIHMS150003},
isbn = {0028-0836},
issn = {0028-0836},
journal = {Nature},
keywords = {Amygdala,Amygdala: physiology,Animal,Animal: physiology,Animals,Anxiety,Anxiety: physiopathology,Avoidance Learning,Behavior,Cues,Electroshock,GABAergic Neurons,GABAergic Neurons: metabolism,Glutamine,Glutamine: metabolism,Inbred C57BL,Male,Mice,Motivation,Motivation: physiology,Optogenetics,Phenotype,Reward,Rhodopsin,Rhodopsin: metabolism,Septal Nuclei,Septal Nuclei: physiology,Ventral Tegmental Area,Ventral Tegmental Area: physiology},
number = {7444},
pages = {224--228},
pmid = {23515155},
title = {{Distinct extended amygdala circuits for divergent motivational states}},
volume = {496},
year = {2013}
}
@article{Jewell2017,
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mendeley-groups = {cnmfe-paper},
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mendeley-groups = {Thesis,cnmfe-paper},
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