Mooney, R. | Search bioRxiv

bioRxiv2018

MIN1PIPE: A Miniscope 1-photon-based Calcium Imaging Signal Extraction Pipeline

In vivo calcium imaging using 1-photon based miniscope and microendoscopic lens enables studies of neural activities in freely behaving animals. However, the high and fluctuating background, the inevitable movements and distortions of imaging field, and the extensive spatial overlaps of fluorescent signals emitted from imaged neurons inherent in this 1-photon imaging method present major challenges for extracting neuronal signals reliably and automatically from the raw imaging data. Here we develop a unifying algorithm called MINiscope 1-photon imaging PIPEline (MIN1PIPE) that contains several standalone modules and can handle a wide range of imaging conditions and qualities with minimal parameter tuning, and automatically and accurately isolate spatially localized neural signals. We quantitatively compare MIN1PIPE with other existing partial methods using both synthetic and real datasets obtained from different animal models, and show that MIN1PIPE has a superior performance both in terms of efficiency and precision in analyzing noisy miniscope calcium imaging data.

neuroscience↗

bioRxiv2018

Identification of midbrain neurons essential for vocal communication

Vocalizations are an essential medium for communication and courtship in numerous mammalian species ranging from mice to humans. In mammals, the midbrain PAG serves as an obligatory node in a vocalization-related network that spans the forebrain and brainstem1-3, as bilateral lesions of the PAG result in mutism2-5. Despite the PAGs importance for vocal production, the identity, function, and connectivity of PAG neurons involved in vocalization has remained elusive, in part because the PAG is a functionally and anatomically heterogeneous structure that serves myriad roles including nociception, defensive behaviors, and autonomic regulation6-9. Here we used a viral genetic \"tagging\" method10,11 to identify a distinct subset of PAG neurons in the male mouse that are selectively activated during the production of ultrasonic vocalizations (USVs) elicited by female cues. Silencing these PAG-USV neurons rendered males mute without affecting their other courtship behaviors and also impaired their ability to attract female mice in a social choice assay. Activating these neurons using chemogenetic or optogenetic methods strongly elevated USV production, even in the absence of female cues. Notably, the timing of individual USVs was entrained to the expiratory phase of breathing but not to the pattern of optogenetic stimulation, suggesting that PAG-USV neural activity initiates and sets the duration of vocal bouts and recruits downstream premotor circuits that precisely pattern vocal output. Consistent with this idea, we found that PAG-USV neurons extend axons into pontine and medullary regions that are speculated to contain premotor central pattern generators important for vocalization3,12,13. These experiments establish the identity of the PAG neurons selectively required for USV production in mice, map their efferent connections, and demonstrate the communicative salience of male USVs in promoting female social affiliation.

neuroscience↗