Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish

Kim, Dal Hyung; Kim, Jungsoo; Marques, João C.; Grama, Abhinav; Hildebrand, David G. C.; Gu, Wenchao; Li, Jennifer M.; Robson, Drew N.

doi:10.1038/nmeth.4429

Cited by 199 publications

(205 citation statements)

References 45 publications

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“…The high volumetric imaging speed and epi-illumination configuration together make LFM a well-suited technique to image freely moving animals, which are of great interests in neuroscience because of the extended behavioral paradigms to understand various complex brain functions 19,[36][37][38][39] . In particular, neural activity in groups of neurons during larval zebrafish's prey capture behavior, which is under extensive investigations [40][41][42][43] , has been recorded at relatively low spatial or temporal resolutions 31,44,45 .…”

Section: Whole Brain Functional Imaging Of Neural Activities In Freelmentioning

confidence: 99%

Capturing volumetric dynamics at high speed in the brain by confocal light field microscopy

Zhang

Bai

Cong

et al. 2020

Preprint

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Neural network performs complex computations through coordinating collective neural dynamics that are fast and in three-dimensions. Meanwhile, its proper function relies on its 3D supporting environment, including the highly dynamic vascular system that drives energy and material flow.Better understanding of these processes requires methods to capture fast volumetric dynamics in thick tissue. This becomes challenging due to the trade-off between speed and optical sectioning capability in conventional imaging techniques. Here we present a new imaging method, confocal light field microscopy, to enable fast volumetric imaging deep into brain. We demonstrated the power of this method by recording whole brain calcium transients in freely swimming larval zebrafish and observed behaviorally correlated activities on single neurons during its prey capture. Furthermore, we captured neural activities and circulating blood cells over a volume ⌀ 800 μm x 150 μm at 70 Hz and up to 600 μm deep in the mice brain.

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Section: Whole Brain Functional Imaging Of Neural Activities In Freelmentioning

confidence: 99%

Capturing volumetric dynamics at high speed in the brain by confocal light field microscopy

Zhang

Bai

Cong

et al. 2020

Preprint

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“…Zebrafish have also been used to study other more complex behaviors such as sleep/wake (Barlow & Rihel, 2017), learning and memory (Gerlai, 2017), locomotion (Müller & van Leeuwen, 2004), and affective depressive-like behaviors and roles of antidepressants (Ziv et al, 2013). Pairing behavioral work with direct imaging of neuronal excitability has recently begun to illuminate the activity of neuronal circuits in mediating the zebrafish behavioral repertoire (Cong et al, 2017;Kim et al, 2017). Pairing behavioral work with direct imaging of neuronal excitability has recently begun to illuminate the activity of neuronal circuits in mediating the zebrafish behavioral repertoire (Cong et al, 2017;Kim et al, 2017).…”

Section: Zebrafish As a Behavioral Modelmentioning

confidence: 99%

“…Current Protocols Essential Laboratory Techniques systems; Pan et al, 2013;Xiong, Obholzer, Noche, & Megason, 2015) will greatly facilitate the ability to describe the full connectome of the zebrafish brain. Similarly, the ability to genetically encode voltage or calcium sensors in distinct neurons or throughout the brain opens tremendous possibilities for recording and manipulating patterns of activity in well-defined circuits or across the whole CNS (Kibat et al, 2016;Kim et al, 2017;Naumann et al, 2016).…”

Section: Of 26mentioning

confidence: 99%

Zebrafish: Development of a Vertebrate Model Organism

Meyers

2018

CP Essential Lab Tech

123

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Zebrafish (Danio rerio) are a small-bodied tropical, freshwater fish species originally from South Asia. The ease of care, year-round prolific breeding, and transparent, external development have made these fish a popular model vertebrate for many fields of biology. Over the past 40 years, the development of methods for genetic and developmental manipulation have driven a rapid rise in their use in research. This review provides an orientation to the zebrafish as a model system, from its ecology and life history to its early use in research and adoption as a key genetic model for vertebrate development. Its current uses and key techniques that highlight future areas of development of the system are also discussed. Finally, an introduction to the essentials of zebrafish use and care are presented, highlighting the ease of adoption of this system for teaching and research use. C 2018 by John Wiley & Sons, Inc.Keywords: zebrafish r Danio rerio r development r model organism r genetics r regeneration r fish

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“…In terms of behaviour larvae exhibit an alternating 23 sequence of movements and pauses, termed bouts. This structure is particularly suited to modular 24 description as individual bouts can be easily segmented and it is relatively easy to acquire many 25 examples from even a single animal due to the high frequency of their movement (Kim et al, 2017). 26…”

Section: Introductionmentioning

confidence: 99%

Hierarchical Compression Reveals Sub-Second to Day-Long Structure in Larval Zebrafish Behaviour

Ghosh

Rihel

2019

Preprint

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Animal behaviour is dynamic, evolving over multiple timescales from milliseconds to days and even across a lifetime. To understand the mechanisms governing these dynamics, it is necessary to capture multi-timescale structure from behavioural data. Here, we develop computational tools and study the behaviour of hundreds of larval zebrafish tracked continuously across multiple 24-hour day/night cycles. We extracted millions of movements and pauses, termed bouts, and used unsupervised learning to reduce each larva's behaviour to an alternating sequence of active and inactive bout types, termed modules. Through hierarchical compression, we identified recurrent behavioural patterns, termed motifs. Module and motif usage varied across the day/night cycle, revealing structure at subsecond to day-long timescales. We further demonstrate that module and motif analysis can uncover novel pharmacological and genetic mutant phenotypes. Overall, our work reveals the organisation of larval zebrafish behaviour at multiple timescales and provides tools to identify structure from largescale behavioural datasets. 2005), the sedating drug, melatonin (Zhdanova et al., 2001), and hypocretin receptor (hcrtr) mutant 59 larva (Yokogawa et al., 2007), loss of which is associated with narcolepsy in humans (Lin et al., 1999) 60 and altered bout structure in zebrafish (Yokogawa et al., 2007; Elbaz et al., 2012). We found that our 61 computational approach could readily detect both compound dose and mutant specific differences in 62 module and motif usage, demonstrating the biological relevance of our behavioural description. 63 64 Ultimately, our work reveals the organisation of larval zebrafish behaviour at sub-second to day-long 65 timescales and provides new computational tools to identify structure from large-scale behavioural 66 datasets. 67 68 69 70 4 Results 71 Behaviour at Scale 72Larval zebrafish behaviour consists of an alternating sequence of movements and pauses, termed 73 bouts, that are organised at sub-second timescales. To capture this structure from high-throughput, 74 long-timescale experiments, we used a 96-well plate set-up with a single larva housed in each well 75 ( Supplementary Figure 1a) and as a proxy for movement recorded the number of pixels that changed 76 intensity within each well between successive pairs of frames, a metric we term Δ pixels. We built on 77 previous work using this set-up (reviewed in: Barlow and Rihel, 2017; Oikonomou and Prober, 2017) 78 by analysing Δ pixels data at 25Hz, rather than in one-minute bins. When recorded in this way, Δ pixels 79 data is an alternating sequence of positive values representing movement magnitude and zeros 80 representing periods of inactivity (Figure 1a, Supplementary video 1). We defined active bouts as any 81 single or consecutive frames with non-zero Δ pixels values and described each bout using several 82 features including the mean and standard deviation of Δ pixels values across the bout (Figure 1a). We 83 defined inactive bouts as any single or conse...

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Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish

Cited by 199 publications

References 45 publications

Capturing volumetric dynamics at high speed in the brain by confocal light field microscopy

Capturing volumetric dynamics at high speed in the brain by confocal light field microscopy

Zebrafish: Development of a Vertebrate Model Organism

Hierarchical Compression Reveals Sub-Second to Day-Long Structure in Larval Zebrafish Behaviour

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