A citation-based method for searching scientific literature

Eftychios A Pnevmatikakis, Daniel Soudry, Yuanjun Gao, Timothy A Machado, Josh Merel, David Pfau, Thomas Reardon, Yu Mu, Clay Lacefield, Weijian Yang, Misha Ahrens, Randy Bruno, Thomas M Jessell, Darcy S Peterka, Rafael Yuste, Liam Paninski. Neuron 2016
Times Cited: 426







List of co-cited articles
805 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


CaImAn an open source tool for scalable calcium imaging data analysis.
Andrea Giovannucci, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon L Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L Gauthier, Pengcheng Zhou,[...]. Elife 2019
221
48

Ultrasensitive fluorescent proteins for imaging neuronal activity.
Tsai-Wen Chen, Trevor J Wardill, Yi Sun, Stefan R Pulver, Sabine L Renninger, Amy Baohan, Eric R Schreiter, Rex A Kerr, Michael B Orger, Vivek Jayaraman,[...]. Nature 2013
41

Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data.
Pengcheng Zhou, Shanna L Resendez, Jose Rodriguez-Romaguera, Jessica C Jimenez, Shay Q Neufeld, Andrea Giovannucci, Johannes Friedrich, Eftychios A Pnevmatikakis, Garret D Stuber, Rene Hen,[...]. Elife 2018
223
37

NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data.
Eftychios A Pnevmatikakis, Andrea Giovannucci. J Neurosci Methods 2017
269
35

Automated analysis of cellular signals from large-scale calcium imaging data.
Eran A Mukamel, Axel Nimmerjahn, Mark J Schnitzer. Neuron 2009
390
29

Miniaturized integration of a fluorescence microscope.
Kunal K Ghosh, Laurie D Burns, Eric D Cocker, Axel Nimmerjahn, Yaniv Ziv, Abbas El Gamal, Mark J Schnitzer. Nat Methods 2011
539
20

Fast online deconvolution of calcium imaging data.
Johannes Friedrich, Pengcheng Zhou, Liam Paninski. PLoS Comput Biol 2017
163
19

High-performance calcium sensors for imaging activity in neuronal populations and microcompartments.
Hod Dana, Yi Sun, Boaz Mohar, Brad K Hulse, Aaron M Kerlin, Jeremy P Hasseman, Getahun Tsegaye, Arthur Tsang, Allan Wong, Ronak Patel,[...]. Nat Methods 2019
369
17

Long-term dynamics of CA1 hippocampal place codes.
Yaniv Ziv, Laurie D Burns, Eric D Cocker, Elizabeth O Hamel, Kunal K Ghosh, Lacey J Kitch, Abbas El Gamal, Mark J Schnitzer. Nat Neurosci 2013
546
17

A shared neural ensemble links distinct contextual memories encoded close in time.
Denise J Cai, Daniel Aharoni, Tristan Shuman, Justin Shobe, Jeremy Biane, Weilin Song, Brandon Wei, Michael Veshkini, Mimi La-Vu, Jerry Lou,[...]. Nature 2016
430
16

Tracking the Same Neurons across Multiple Days in Ca2+ Imaging Data.
Liron Sheintuch, Alon Rubin, Noa Brande-Eilat, Nitzan Geva, Noa Sadeh, Or Pinchasof, Yaniv Ziv. Cell Rep 2017
101
15

Thy1-GCaMP6 transgenic mice for neuronal population imaging in vivo.
Hod Dana, Tsai-Wen Chen, Amy Hu, Brenda C Shields, Caiying Guo, Loren L Looger, Douglas S Kim, Karel Svoboda. PLoS One 2014
273
14

Detecting cells using non-negative matrix factorization on calcium imaging data.
Ryuichi Maruyama, Kazuma Maeda, Hajime Moroda, Ichiro Kato, Masashi Inoue, Hiroyoshi Miyakawa, Toru Aonishi. Neural Netw 2014
58
24

Spontaneous behaviors drive multidimensional, brainwide activity.
Carsen Stringer, Marius Pachitariu, Nicholas Steinmetz, Charu Bai Reddy, Matteo Carandini, Kenneth D Harris. Science 2019
399
13

DeepLabCut: markerless pose estimation of user-defined body parts with deep learning.
Alexander Mathis, Pranav Mamidanna, Kevin M Cury, Taiga Abe, Venkatesh N Murthy, Mackenzie Weygandt Mathis, Matthias Bethge. Nat Neurosci 2018
941
12

Single-trial neural dynamics are dominated by richly varied movements.
Simon Musall, Matthew T Kaufman, Ashley L Juavinett, Steven Gluf, Anne K Churchland. Nat Neurosci 2019
273
12

A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging.
Nicholas James Sofroniew, Daniel Flickinger, Jonathan King, Karel Svoboda. Elife 2016
272
12

Two-photon laser scanning fluorescence microscopy.
W Denk, J H Strickler, W W Webb. Science 1990
11

Analysis pipelines for calcium imaging data.
Eftychios A Pnevmatikakis. Curr Opin Neurobiol 2019
30
33

Fully integrated silicon probes for high-density recording of neural activity.
James J Jun, Nicholas A Steinmetz, Joshua H Siegle, Daniel J Denman, Marius Bauza, Brian Barbarits, Albert K Lee, Costas A Anastassiou, Alexandru Andrei, Çağatay Aydın,[...]. Nature 2017
687
9

Imaging calcium in neurons.
Christine Grienberger, Arthur Konnerth. Neuron 2012
669
9

Simultaneous Multi-plane Imaging of Neural Circuits.
Weijian Yang, Jae-Eun Kang Miller, Luis Carrillo-Reid, Eftychios Pnevmatikakis, Liam Paninski, Rafael Yuste, Darcy S Peterka. Neuron 2016
122
9

MIN1PIPE: A Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline.
Jinghao Lu, Chunyuan Li, Jonnathan Singh-Alvarado, Zhe Charles Zhou, Flavio Fröhlich, Richard Mooney, Fan Wang. Cell Rep 2018
54
16

Sensitive red protein calcium indicators for imaging neural activity.
Hod Dana, Boaz Mohar, Yi Sun, Sujatha Narayan, Andrew Gordus, Jeremy P Hasseman, Getahun Tsegaye, Graham T Holt, Amy Hu, Deepika Walpita,[...]. Elife 2016
475
9

Imaging Cortical Dynamics in GCaMP Transgenic Rats with a Head-Mounted Widefield Macroscope.
Benjamin B Scott, Stephan Y Thiberge, Caiying Guo, D Gowanlock R Tervo, Carlos D Brody, Alla Y Karpova, David W Tank. Neuron 2018
63
14

Fast nonnegative deconvolution for spike train inference from population calcium imaging.
Joshua T Vogelstein, Adam M Packer, Timothy A Machado, Tanya Sippy, Baktash Babadi, Rafael Yuste, Liam Paninski. J Neurophysiol 2010
233
9

Imaging large-scale neural activity with cellular resolution in awake, mobile mice.
Daniel A Dombeck, Anton N Khabbaz, Forrest Collman, Thomas L Adelman, David W Tank. Neuron 2007
671
9

Dynamic Reorganization of Neuronal Activity Patterns in Parietal Cortex.
Laura N Driscoll, Noah L Pettit, Matthias Minderer, Selmaan N Chettih, Christopher D Harvey. Cell 2017
141
9

ABLE: An Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data.
Stephanie Reynolds, Therese Abrahamsson, Renaud Schuck, P Jesper Sjöström, Simon R Schultz, Pier Luigi Dragotti. eNeuro 2017
21
42

Fast and robust active neuron segmentation in two-photon calcium imaging using spatiotemporal deep learning.
Somayyeh Soltanian-Zadeh, Kaan Sahingur, Sarah Blau, Yiyang Gong, Sina Farsiu. Proc Natl Acad Sci U S A 2019
50
18


Breakdown of spatial coding and interneuron synchronization in epileptic mice.
Tristan Shuman, Daniel Aharoni, Denise J Cai, Christopher R Lee, Spyridon Chavlis, Lucia Page-Harley, Lauren M Vetere, Yu Feng, Chen Yi Yang, Irene Mollinedo-Gajate,[...]. Nat Neurosci 2020
59
13

In vivo imaging of neural activity.
Weijian Yang, Rafael Yuste. Nat Methods 2017
191
8

Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance.
Linda Madisen, Aleena R Garner, Daisuke Shimaoka, Amy S Chuong, Nathan C Klapoetke, Lu Li, Alexander van der Bourg, Yusuke Niino, Ladan Egolf, Claudio Monetti,[...]. Neuron 2015
579
8

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
8

SIMA: Python software for analysis of dynamic fluorescence imaging data.
Patrick Kaifosh, Jeffrey D Zaremba, Nathan B Danielson, Attila Losonczy. Front Neuroinform 2014
104
8

A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology.
Ziqiang Wei, Bei-Jung Lin, Tsai-Wen Chen, Kayvon Daie, Karel Svoboda, Shaul Druckmann. PLoS Comput Biol 2020
45
17

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice.
Lawrence Huang, Peter Ledochowitsch, Ulf Knoblich, Jérôme Lecoq, Gabe J Murphy, R Clay Reid, Saskia Ej de Vries, Christof Koch, Hongkui Zeng, Michael A Buice,[...]. Elife 2021
49
16

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.
Ahmed S Abdelfattah, Takashi Kawashima, Amrita Singh, Ondrej Novak, Hui Liu, Yichun Shuai, Yi-Chieh Huang, Luke Campagnola, Stephanie C Seeman, Jianing Yu,[...]. Science 2019
181
7

Spatio-temporal correlations and visual signalling in a complete neuronal population.
Jonathan W Pillow, Jonathon Shlens, Liam Paninski, Alexander Sher, Alan M Litke, E J Chichilnisky, Eero P Simoncelli. Nature 2008
659
7

Whole-brain functional imaging at cellular resolution using light-sheet microscopy.
Misha B Ahrens, Michael B Orger, Drew N Robson, Jennifer M Li, Philipp J Keller. Nat Methods 2013
681
7

A pyramid approach to subpixel registration based on intensity.
P Thévenaz, U E Ruttimann, M Unser. IEEE Trans Image Process 1998
7

NINscope, a versatile miniscope for multi-region circuit investigations.
Andres de Groot, Bastijn JG van den Boom, Romano M van Genderen, Joris Coppens, John van Veldhuijzen, Joop Bos, Hugo Hoedemaker, Mario Negrello, Ingo Willuhn, Chris I De Zeeuw,[...]. Elife 2020
50
14

Deep tissue two-photon microscopy.
Fritjof Helmchen, Winfried Denk. Nat Methods 2005
7

Controlling Visually Guided Behavior by Holographic Recalling of Cortical Ensembles.
Luis Carrillo-Reid, Shuting Han, Weijian Yang, Alejandro Akrouh, Rafael Yuste. Cell 2019
121
7

Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.
Shreya Saxena, Ian Kinsella, Simon Musall, Sharon H Kim, Jozsef Meszaros, David N Thibodeaux, Carla Kim, John Cunningham, Elizabeth M C Hillman, Anne Churchland,[...]. PLoS Comput Biol 2020
25
28

Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods.
Alexander Song, Jeff L Gauthier, Jonathan W Pillow, David W Tank, Adam S Charles. J Neurosci Methods 2021
16
43

The reorganization and reactivation of hippocampal maps predict spatial memory performance.
David Dupret, Joseph O'Neill, Barty Pleydell-Bouverie, Jozsef Csicsvari. Nat Neurosci 2010
382
7

Efficient subpixel image registration algorithms.
Manuel Guizar-Sicairos, Samuel T Thurman, James R Fienup. Opt Lett 2008
671
7

FISSA: A neuropil decontamination toolbox for calcium imaging signals.
Sander W Keemink, Scott C Lowe, Janelle M P Pakan, Evelyn Dylda, Mark C W van Rossum, Nathalie L Rochefort. Sci Rep 2018
39
17


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.