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
Times Cited: 426
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
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
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
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
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
37
NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data.
Eftychios A Pnevmatikakis, Andrea Giovannucci. J Neurosci Methods 2017
Eftychios A Pnevmatikakis, Andrea Giovannucci. J Neurosci Methods 2017
35
Automated analysis of cellular signals from large-scale calcium imaging data.
Eran A Mukamel, Axel Nimmerjahn, Mark J Schnitzer. Neuron 2009
Eran A Mukamel, Axel Nimmerjahn, Mark J Schnitzer. Neuron 2009
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
Kunal K Ghosh, Laurie D Burns, Eric D Cocker, Axel Nimmerjahn, Yaniv Ziv, Abbas El Gamal, Mark J Schnitzer. Nat Methods 2011
20
Fast online deconvolution of calcium imaging data.
Johannes Friedrich, Pengcheng Zhou, Liam Paninski. PLoS Comput Biol 2017
Johannes Friedrich, Pengcheng Zhou, Liam Paninski. PLoS Comput Biol 2017
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
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
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
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
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
Denise J Cai, Daniel Aharoni, Tristan Shuman, Justin Shobe, Jeremy Biane, Weilin Song, Brandon Wei, Michael Veshkini, Mimi La-Vu, Jerry Lou,[...]. Nature 2016
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
Liron Sheintuch, Alon Rubin, Noa Brande-Eilat, Nitzan Geva, Noa Sadeh, Or Pinchasof, Yaniv Ziv. Cell Rep 2017
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
Hod Dana, Tsai-Wen Chen, Amy Hu, Brenda C Shields, Caiying Guo, Loren L Looger, Douglas S Kim, Karel Svoboda. PLoS One 2014
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
Ryuichi Maruyama, Kazuma Maeda, Hajime Moroda, Ichiro Kato, Masashi Inoue, Hiroyoshi Miyakawa, Toru Aonishi. Neural Netw 2014
24
Spontaneous behaviors drive multidimensional, brainwide activity.
Carsen Stringer, Marius Pachitariu, Nicholas Steinmetz, Charu Bai Reddy, Matteo Carandini, Kenneth D Harris. Science 2019
Carsen Stringer, Marius Pachitariu, Nicholas Steinmetz, Charu Bai Reddy, Matteo Carandini, Kenneth D Harris. Science 2019
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
Alexander Mathis, Pranav Mamidanna, Kevin M Cury, Taiga Abe, Venkatesh N Murthy, Mackenzie Weygandt Mathis, Matthias Bethge. Nat Neurosci 2018
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
Simon Musall, Matthew T Kaufman, Ashley L Juavinett, Steven Gluf, Anne K Churchland. Nat Neurosci 2019
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
Nicholas James Sofroniew, Daniel Flickinger, Jonathan King, Karel Svoboda. Elife 2016
12
Two-photon laser scanning fluorescence microscopy.
W Denk, J H Strickler, W W Webb. Science 1990
W Denk, J H Strickler, W W Webb. Science 1990
11
Analysis pipelines for calcium imaging data.
Eftychios A Pnevmatikakis. Curr Opin Neurobiol 2019
Eftychios A Pnevmatikakis. Curr Opin Neurobiol 2019
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
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
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
Weijian Yang, Jae-Eun Kang Miller, Luis Carrillo-Reid, Eftychios Pnevmatikakis, Liam Paninski, Rafael Yuste, Darcy S Peterka. Neuron 2016
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
Jinghao Lu, Chunyuan Li, Jonnathan Singh-Alvarado, Zhe Charles Zhou, Flavio Fröhlich, Richard Mooney, Fan Wang. Cell Rep 2018
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
Hod Dana, Boaz Mohar, Yi Sun, Sujatha Narayan, Andrew Gordus, Jeremy P Hasseman, Getahun Tsegaye, Graham T Holt, Amy Hu, Deepika Walpita,[...]. Elife 2016
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
Benjamin B Scott, Stephan Y Thiberge, Caiying Guo, D Gowanlock R Tervo, Carlos D Brody, Alla Y Karpova, David W Tank. Neuron 2018
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
Joshua T Vogelstein, Adam M Packer, Timothy A Machado, Tanya Sippy, Baktash Babadi, Rafael Yuste, Liam Paninski. J Neurophysiol 2010
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
Daniel A Dombeck, Anton N Khabbaz, Forrest Collman, Thomas L Adelman, David W Tank. Neuron 2007
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
Laura N Driscoll, Noah L Pettit, Matthias Minderer, Selmaan N Chettih, Christopher D Harvey. Cell 2017
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
Stephanie Reynolds, Therese Abrahamsson, Renaud Schuck, P Jesper Sjöström, Simon R Schultz, Pier Luigi Dragotti. eNeuro 2017
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
Somayyeh Soltanian-Zadeh, Kaan Sahingur, Sarah Blau, Yiyang Gong, Sina Farsiu. Proc Natl Acad Sci U S A 2019
18
The hippocampus as a spatial map. Preliminary evidence from unit activity in the freely-moving rat.
J O'Keefe, J Dostrovsky. Brain Res 1971
J O'Keefe, J Dostrovsky. Brain Res 1971
8
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
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
13
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
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
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
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
Patrick Kaifosh, Jeffrey D Zaremba, Nathan B Danielson, Attila Losonczy. Front Neuroinform 2014
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
Ziqiang Wei, Bei-Jung Lin, Tsai-Wen Chen, Kayvon Daie, Karel Svoboda, Shaul Druckmann. PLoS Comput Biol 2020
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
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
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
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
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
Jonathan W Pillow, Jonathon Shlens, Liam Paninski, Alexander Sher, Alan M Litke, E J Chichilnisky, Eero P Simoncelli. Nature 2008
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
Misha B Ahrens, Michael B Orger, Drew N Robson, Jennifer M Li, Philipp J Keller. Nat Methods 2013
7
A pyramid approach to subpixel registration based on intensity.
P Thévenaz, U E Ruttimann, M Unser. IEEE Trans Image Process 1998
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
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
14
Controlling Visually Guided Behavior by Holographic Recalling of Cortical Ensembles.
Luis Carrillo-Reid, Shuting Han, Weijian Yang, Alejandro Akrouh, Rafael Yuste. Cell 2019
Luis Carrillo-Reid, Shuting Han, Weijian Yang, Alejandro Akrouh, Rafael Yuste. Cell 2019
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
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
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
Alexander Song, Jeff L Gauthier, Jonathan W Pillow, David W Tank, Adam S Charles. J Neurosci Methods 2021
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
David Dupret, Joseph O'Neill, Barty Pleydell-Bouverie, Jozsef Csicsvari. Nat Neurosci 2010
7
Efficient subpixel image registration algorithms.
Manuel Guizar-Sicairos, Samuel T Thurman, James R Fienup. Opt Lett 2008
Manuel Guizar-Sicairos, Samuel T Thurman, James R Fienup. Opt Lett 2008
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
Sander W Keemink, Scott C Lowe, Janelle M P Pakan, Evelyn Dylda, Mark C W van Rossum, Nathalie L Rochefort. Sci Rep 2018
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.