Bonsai: An event-based framework for processing and controlling data streams

Lopes, Gonçalo; Bonacchi, Niccolò; Frazão, João; Neto, Joana P.; Atallah, Bassam V.; Soares, Sofia; Moreira, Luís; Matias, Sara; Itskov, Pavel M.; Correia, Patrícia A.; Medina, Roberto E.; Calcaterra, Lorenza; Dreosti, Elena; Paton, Joseph J.; Kampff, Adam R.

doi:10.1101/006791

Cited by 38 publications

(47 citation statements)

References 10 publications

(15 reference statements)

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“…Video data with timestamps for the two eyes and overhead camera were acquired at 30 frames per second using Bonsai [26] . We used DeepLabCut [27] for markerless estimation of mouse and cricket position from overhead videos.…”

Section: Mouse and Cricket Trackingmentioning

confidence: 99%

Dynamics of gaze control during prey capture in freely moving mice

Michaiel

Abe

Niell

2020

Preprint

102

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Many studies of visual processing are conducted in unnatural conditions, such as head-and gaze-fixation.As this radically limits natural exploration of the visual environment, there is much less known about how animals actively use their sensory systems to acquire visual information in natural, goal-directed contexts.Recently, prey capture has emerged as an ethologically relevant behavior that mice perform without training, and that engages vision for accurate orienting and pursuit. However, it is unclear how mice target their gaze during such natural behaviors, particularly since, in contrast to many predatory species, mice have a narrow binocular field and lack foveate vision that would entail fixing their gaze on a specific point in the visual field. Here we measured head and bilateral eye movements in freely moving mice performing prey capture. We find that the majority of eye movements are compensatory for head movements, thereby acting to stabilize the visual scene. During head turns, however, these periods of stabilization are interspersed with non-compensatory saccades that abruptly shift gaze position. Analysis of eye movements relative to the cricket position shows that the saccades do not preferentially select a specific point in the visual scene. Rather, orienting movements are driven by the head, with the eyes following in coordination to sequentially stabilize and recenter the gaze. These findings help relate eye movements in the mouse to other species, and provide a foundation for studying active vision during ethological behaviors in the mouse.

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Section: Mouse and Cricket Trackingmentioning

confidence: 99%

Dynamics of gaze control during prey capture in freely moving mice

Michaiel

Abe

Niell

2020

Preprint

102

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“…All trials were recorded with a Raspberry Pi 3B+ equipped with a V1 camera module (https://www.raspberrypi.org/documentation/hardware/camera/) and using Raspivid version 1.3.12 as 1296x972 pixel, 30 frame/second MP4 video files. Automated analysis was carried out with custom scripts written in Bonsai version 2.4-preview (Lopes et al, 2015). A researcher blinded to the treatment assessed and scored the exploration time manually after automated analysis.…”

Section: Rnamentioning

confidence: 99%

In vivo CRISPRa decreases seizures and rescues cognitive deficits in a rodent model of epilepsy

Colasante

Qiu

Massimino

et al. 2018

Preprint

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Epilepsy is a major health burden, calling for new mechanistic and therapeutic insights.CRISPR-mediated gene editing shows promise to cure genetic pathologies, although hitherto it has mostly been applied ex-vivo. Its translational potential for treating non-genetic pathologies is still unexplored. Furthermore, neurological diseases represent an important challenge for the application of CRISPR, because of the need in many cases to manipulate gene function of neurons in situ. A variant of CRISPR, CRISPRa, offers the possibility to modulate the expression of endogenous genes by directly targeting their promoters. We asked if this strategy can effectively treat acquired focal epilepsy, focusing on ion channels because their manipulation is known be effective in changing network hyperactivity and hypersynchronisation. We applied a doxycycline-inducible CRISPRa technology to increase the expression of the potassium channel gene Kcna1 (encoding Kv1.1) in mouse hippocampal excitatory neurons. CRISPRa-mediated Kv1.1 upregulation led to a substantial decrease in neuronal excitability. Continuous video-EEG telemetry showed that AAV9-mediated delivery of CRISPRa, upon doxycycline administration, decreased spontaneous generalized tonicclonic seizures in a model of temporal lobe epilepsy, and rescued cognitive impairment and transcriptomic alterations associated with chronic epilepsy. The focal treatment minimizes concerns about off-target effects in other organs and brain areas. This study provides the proof of principle for a translational CRISPR-based approach to treat neurological diseases characterized by abnormal circuit excitability.

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“…Video recording was performed using a Sony camera (HDR HC7E) connected to a computer running Virtual Dub software to acquire images. Off-line analysis of videos was performed using Bonsai [11] and the behaviour of the female was analysed using MATLAB. The latency of first entry, the number of entries and re-entries (when the female returns to the same male's compartment) into the male's compartment, as well as the time spent in each male box were scored.…”

Section: Behavioural Analysismentioning

confidence: 99%

Sexual imprinting overrides order effects

Lima

Moreira

Zinck

et al. 2019

Preprint

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Mate choice is a complex decision that requires the integration of cues from potential mates with individual preferences. Choosers' preferences are shaped by recent events, early life experience and by the evolutionary history of its own species. To better understand the interaction between these factors, we studied mate choice in the female house mouse, Mus musculus. Females of one of the musculus subspecies, Mus musculus musculus, show preference for males of their own subspecies compared to males of the sibling subspecies, Mus musculus domesticus. Such an assortative preference is ecologically relevant at contact zones, where it contributes to the reproductive isolation of sympatric populations and can be reproduced in controlled laboratory conditions, but its origins are still under debate. Here, we show that female mouse mate choice depends on both early postnatal life experience and the order of prospective mates encountered as an adult and that these effects interact asymmetrically. Whereas females raised in their normal M. m. musculus environment display a robust assortative preference, females fostered in a M. m. domesticus family prefer the first male encountered, regardless of subspecies. Thus, early life experience of M. m. musculus females, when concordant with genetic self-identity, overrides sampling order effects, ensuring robust assortative choice. In the absence of this match between phylogeny and early life experience, first impression effects dominate mate choice. Assortative mate choice is one of the mechanisms underlying the reproductive isolation between the two subspecies of house mouse, M. m. musculus and M. m. domesticus. These two lineages diverged from a common Asian ancestor which followed different human migratory routes and have subsequently established a secondary contact zone in central Europe [1], where they exhibit asymmetric mate preference: M. m. musculus females prefer their own subspecies, whereas M. m. domesticus females mate indiscriminately with both [2]. Using inbred strains of wild-derived mice as representatives of the M. m. musculus subspecies and laboratory mice as representatives of M. m. domesticus, the preference of M. m. musculus females can be studied under laboratory conditions,

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Bonsai: An event-based framework for processing and controlling data streams

Cited by 38 publications

References 10 publications

Dynamics of gaze control during prey capture in freely moving mice

Dynamics of gaze control during prey capture in freely moving mice

In vivo CRISPRa decreases seizures and rescues cognitive deficits in a rodent model of epilepsy

Sexual imprinting overrides order effects

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