A standardized head-fixation system for performing large-scale,in vivophysiological recordings in mice

Abstract

12The Allen Institute recently built a set of high-throughput experimental pipelines to 13 collect comprehensive in vivo surveys of physiological activity in the visual cortex of awake, 14head-fixed mice. Developing these large-scale, industrial-like pipelines posed many scientific, 15operational, and engineering challenges. Here we describe our strategies for collecting 16standardized, multi-modal in vivo datasets across many instrumental platforms over long 17 periods of time. Our goal of creating a cross-platform reference space to which all pipeline 18 datasets were mapped required development of 1) a robust headframe, 2) a reproducible 19clamping system, and 3) data-collection systems that are built, and maintained, around precise 20 alignment with a reference artifact. When paired with our pipeline clamping system, the Allen 21Brain Observatory headframe exceeded deflection and reproducibility requirements. All 22 headframe, surgical tooling, and clamp design documentation have been made freely available 23 as an open resource to the scientific community. 24 65

WITHDRAWN: Multiplane Mesoscope reveals distinct cortical interactions following expectation violations

“…Surgical headpost and cranial window implantation was performed as described elsewhere 25,34,38 . Headpost and cranial window surgery was performed on healthy mice that ranged in age from p35 to p60, weighing no less than 15 g at time of surgery.…”

“…After a 1–2 week recovery from surgery, animals underwent intrinsic signal imaging for retinotopic mapping, and then entered into behavioral training. Custom tools and implants used in the surgery were designed at the Allen Institute and are described in detail elsewhere 38 .…”

Measuring stimulus-evoked neurophysiological differentiation in distinct populations of neurons in mouse visual cortex

“…Experimental design. (A) Data were acquired using the AIBS' standardized two-photon calcium imaging pipeline (de Vries et al, 2020;Groblewski et al, 2020;see Methods). Briefly, a custom headframe was implanted; intrinsic signal imaging (ISI) was performed to delineate 6 retinotopically mapped visual areas; the mouse was habituated to the passive viewing paradigm over the course of ~2 weeks; and two-photon calcium imaging was performed in the left visual cortex while animals viewed stimuli presented to the contralateral eye in several experimental sessions.…”

“…The AIBS optical physiology pipeline is described in detail in de Vries et al 2020and Groblewski et al (2020). Analysis was performed with custom Python and R code using numpy (C. R. Harris et al, 2020), scipy (Virtanen et al, 2020), pandas (Reback et al, 2020), scikitlearn (Pedregosa et al, 2011), matplotlib (Hunter, 2007), seaborn (Waskom & the seaborn development team, 2020), lme4 (Bates et al, 2015, p. 4), multcomp (Hothorn et al, 2008), and…”

Characterization of Learning, Motivation, and Visual Perception in Five Transgenic Mouse Lines Expressing GCaMP in Distinct Cell Populations

“…Some of the mice included in this study were later used in a set of 2-photon calcium imaging experiments (Garrett et al, 2020) and, as such, they all initially received a headpost and cranial window surgery as previously described (De Vries et al, 2020;Groblewski et al, 2020a). Briefly, surgery was performed on healthy mice that ranged in age from 5 to 12 weeks.…”