CAVE: An Open-Source Tool for Combined Analysis of Head-Mounted Calcium Imaging and Behavior in MATLAB by Jennifer Tegtmeier, Marcel Brosch, Marcel Brosch, Kathrin Janitzky, Kathrin Janitzky, Hans-Jochen Heinze, Hans-Jochen Heinze, Hans-Jochen Heinze, Frank W. Ohl, Frank W. Ohl, Frank W. Ohl, Michael T. Lippert, Michael T. Lippert

Subjects: “…single-photon head-mounted calcium imaging…”
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Identification of Neuronal Network Properties from the Spectral Analysis of Calcium Imaging Signals in Neuronal Cultures by Elisenda eTibau, Miguel eValencia, Jordi eSoriano

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Simultaneous dendritic voltage and calcium imaging and somatic recording from Purkinje neurons in awake mice by Christopher J. Roome, Bernd Kuhn

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Longitudinal two-photon calcium imaging with ultra-large cranial window for head-fixed mice by Ryoma Hattori, Takaki Komiyama

“…Here, we describe a protocol for longitudinal in vivo two-photon calcium imaging with an ultra-large cranial window that exposes most of the dorsal cortex in head-fixed mice. …”
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Timescale of hole closure during plasma membrane repair estimated by calcium imaging and numerical modeling by Martin Berg Klenow, Anne Sofie Busk Heitmann, Jesper Nylandsted, Adam Cohen Simonsen

“…Repair consists of sequential steps, with closure of the membrane hole being the key event that allows the cell to recover, thus identifying the kinetics of hole closure as important for clarifying repair mechanisms and as a quantitative handle on repair efficiency. We implement calcium imaging in MCF7 breast carcinoma cells subject to laser damage, coupled with a model describing the spatio-temporal calcium distribution. …”
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High resolution ultrasonic neural modulation observed via in vivo two-photon calcium imaging by Zongyue Cheng, Chenmao Wang, Bowen Wei, Wenbiao Gan, Qifa Zhou, Meng Cui

“…To investigate the neuronal response at cellular resolutions, we developed a dual-modality system combining in vivo two-photon calcium imaging and focused ultrasound modulation. The studies show that the ∼30 MHz ultrasound can suppress the neuronal activity in awake mice at 100-μm scale spatial resolutions, paving the way for high-resolution ultrasonic neural modulation. …”
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Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference. by Vahid Rahmati, Knut Kirmse, Dimitrije Marković, Knut Holthoff, Stefan J Kiebel

“…Calcium imaging has been used as a promising technique to monitor the dynamic activity of neuronal populations. …”
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Non-invasive phenotyping and drug testing in single cardiomyocytes or beta-cells by calcium imaging and optogenetics by Chang, Y, Broyles, C, Brook, F, Davies, M, Turtle, C, Nagai, T, Daniels, M

Genetically engineered mice for combinatorial cardiovascular optobiology by Frank K Lee, Jane C Lee, Bo Shui, Shaun Reining, Megan Jibilian, David M Small, Jason S Jones, Nathaniel H Allan-Rahill, Michael RE Lamont, Megan A Rizzo, Sendoa Tajada, Manuel F Navedo, Luis Fernando Santana, Nozomi Nishimura, Michael I Kotlikoff

Subjects: “…calcium imaging…”
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PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening by Elena Artimovich, Russell K. Jackson, Michaela B. C. Kilander, Yu-Chih Lin, Michael W. Nestor

Subjects: “…Calcium imaging software…”
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In vivo calcium imaging reveals disordered interictal network dynamics in epileptic stxbp1b zebrafish by Jing Liu, Kathryn A. Salvati, Scott C. Baraban

“…To study these networks in the context of STXBP1 mutations, we combine a larval zebrafish model with in vivo fast confocal calcium imaging and extracellular local field potential recordings. …”
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Hippocampal cognitive and relational map paradigms explored by multisensory encoding recording with wide-field calcium imaging by Dechuan Sun, Noor E. Karishma Shaik, Ranjith Rajasekharan Unnithan, Chris French

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End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging. by Takehiro Ajioka, Nobuhiro Nakai, Okito Yamashita, Toru Takumi

“…In this study, we examine the performance of deep learning to classify mouse behavioral states from mesoscopic cortex-wide calcium imaging data. Our convolutional neural network (CNN)-based end-to-end decoder combined with recurrent neural network (RNN) classifies the behavioral states with high accuracy and robustness to individual differences on temporal scales of sub-seconds. …”
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Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. by Philipp Berens, Jeremy Freeman, Thomas Deneux, Nikolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H Macke, Srinivas C Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D Harris, Ben Bolte, Timothy A Machado, Dario Ringach, Jasmine Stone, Luke E Rogerson, Nicolas J Sofroniew, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S Tolias, Matthias Bethge

“…In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. …”
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Combined segmentation and classification-based approach to automated analysis of biomedical signals obtained from calcium imaging. by Gizem Dursun, Dunja Bijelić, Neşe Ayşit, Burcu Kurt Vatandaşlar, Lidija Radenović, Abdulkerim Çapar, Bilal Ersen Kerman, Pavle R Andjus, Andrej Korenić, Ufuk Özkaya

“…We propose a segmentation and classification-based approach for assembling an automated screening system for the analysis of calcium imaging. The method was developed and verified using the effects of disease IgGs (from Amyotrophic Lateral Sclerosis patients) on calcium (Ca2+) homeostasis. …”
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Prediction of Forelimb Reach Results From Motor Cortex Activities Based on Calcium Imaging and Deep Learning by Chunyue Li, Danny C. W. Chan, Xiaofeng Yang, Ya Ke, Wing-Ho Yung

“…Here, we ask if calcium imaging data recorded by TPM in rodent brain can provide enough information to predict features of upcoming movement. …”
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Cardioluminescence in Transgenic Zebrafish Larvae: A Calcium Imaging Tool to Study Drug Effects and Pathological Modeling by Manuel Vicente, Jussep Salgado-Almario, Michelle M. Collins, Antonio Martínez-Sielva, Masafumi Minoshima, Kazuya Kikuchi, Beatriz Domingo, Juan Llopis

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Correction: Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference. by PLOS Computational Biology Staff

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Real-Time Processing of Two-Photon Calcium Imaging Data Including Lateral Motion Artifact Correction by Akinori Mitani, Takaki Komiyama

Subjects: “…two-photon calcium imaging…”
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Direct extraction of signal and noise correlations from two-photon calcium imaging of ensemble neuronal activity by Anuththara Rupasinghe, Nikolas Francis, Ji Liu, Zac Bowen, Patrick O Kanold, Behtash Babadi

“…While two-photon calcium imaging has created a unique opportunity to record the activity of large populations of neurons, existing methods for inferring correlations from these data face several challenges. …”
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