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Bennett C, Ouellette B, Ramirez TK, Cahoon A, Cabasco H, Browning Y, Lakunina A, Lynch GF, McBride EG, Belski H, Gillis R, Grasso C, Howard R, Johnson T, Loeffler H, Smith H, Sullivan D, Williford A, Caldejon S, Durand S, Gale S, Guthrie A, Ha V, Han W, Hardcastle B, Mochizuki C, Sridhar A, Suarez L, Swapp J, Wilkes J, Siegle JH, Farrell C, Groblewski PA, Olsen SR. SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain. Neuron 2024; 112:2869-2885.e8. [PMID: 38996587 DOI: 10.1016/j.neuron.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/02/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
To understand the neural basis of behavior, it is essential to measure spiking dynamics across many interacting brain regions. Although new technologies, such as Neuropixels probes, facilitate multi-regional recordings, significant surgical and procedural hurdles remain for these experiments to achieve their full potential. Here, we describe skull-shaped hemispheric implants enabling large-scale electrophysiology datasets (SHIELD). These 3D-printed skull-replacement implants feature customizable insertion holes, allowing dozens of cortical and subcortical structures to be recorded in a single mouse using repeated multi-probe insertions over many days. We demonstrate the procedure's high success rate, biocompatibility, lack of adverse effects on behavior, and compatibility with imaging and optogenetics. To showcase SHIELD's scientific utility, we use multi-probe recordings to reveal novel insights into how alpha rhythms organize spiking activity across visual and sensorimotor networks. Overall, this method enables powerful, large-scale electrophysiological experiments for the study of distributed neural computation.
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Affiliation(s)
- Corbett Bennett
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA.
| | - Ben Ouellette
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | | | | | - Hannah Cabasco
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Yoni Browning
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Anna Lakunina
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Galen F Lynch
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | | | - Hannah Belski
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Ryan Gillis
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Conor Grasso
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Robert Howard
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Tye Johnson
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Henry Loeffler
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Heston Smith
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | | | | | | | | | - Samuel Gale
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Alan Guthrie
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Vivian Ha
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Warren Han
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Ben Hardcastle
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | | | - Arjun Sridhar
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Lucas Suarez
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Jackie Swapp
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Joshua Wilkes
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | | | | | | | - Shawn R Olsen
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA.
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Weaver IA, Aryana Yousefzadeh S, Tadross MR. An open-source head-fixation and implant-protection system for mice. HARDWAREX 2023; 13:e00391. [PMID: 36632413 PMCID: PMC9826893 DOI: 10.1016/j.ohx.2022.e00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/21/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Mice are widely used in neuroscience experiments, which often require head-fixation and attachment of skull-mounted hardware. For many experiments, these components must remain intact over weeks to months, ideally with animals group housed. Many labs have designed ad-hoc head-fixation systems, which is an inefficient process. For example, when reinventing these solutions in our lab, we faced challenges with group housing, wherein mice would chew and damage implanted cannulas and electrodes of their cage mates. We performed several non-trivial design iterations to solve this problem, and present the most successful designs as an open-source collection. The designs include a standard mounting headbar compatible with most skull-mounted hardware, a snap-on protective mouse hat (headhat) to prevent mice from chewing the hardware, and a head-fixation station to facilitate common experimental procedures. We provide 3D-printing files, detail vendors and software used to make the components of the system, and provide editable design files for maximum flexibility to individual lab requirements.
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Durand S, Heller GR, Ramirez TK, Luviano JA, Williford A, Sullivan DT, Cahoon AJ, Farrell C, Groblewski PA, Bennett C, Siegle JH, Olsen SR. Acute head-fixed recordings in awake mice with multiple Neuropixels probes. Nat Protoc 2023; 18:424-457. [PMID: 36477710 DOI: 10.1038/s41596-022-00768-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/09/2022] [Indexed: 12/12/2022]
Abstract
Multi-electrode arrays such as Neuropixels probes enable electrophysiological recordings from large populations of single neurons with high temporal resolution. By using such probes, the activity from functionally interacting, yet distinct, brain regions can be measured simultaneously by inserting multiple probes into the same subject. However, the use of multiple probes in small animals such as mice requires the removal of a sizable fraction of the skull, while also minimizing tissue damage and keeping the brain stable during the recordings. Here, we describe a step-by-step process designed to facilitate reliable recordings from up to six Neuropixels probes simultaneously in awake, head-fixed mice. The procedure involves four stages: the implantation of a headframe and a removable glass coverslip, the precise positioning of the Neuropixels probes at targeted points on the brain surface, the placement of a perforated plastic imaging window and the insertion of the probes into the brain of an awake mouse. The approach provides access to multiple brain regions and has been successfully applied across hundreds of mice. The procedure has been optimized for dense recordings from the mouse visual system, but it can be adapted for alternative recording configurations to target multiple probes in other brain areas. The protocol is suitable for users with experience in stereotaxic surgery in mice.
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Affiliation(s)
| | - Greggory R Heller
- Allen Institute, Seattle, WA, USA.,Department of Brain and Cognitive Sciences, Massachussetts Institute of Technology, Cambridge, MA, USA
| | - Tamina K Ramirez
- Allen Institute, Seattle, WA, USA.,Department of Neurobiology and Behavior, Columbia University, New York, NY, USA
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Yoon Y, Shin H, Byun D, Woo J, Cho Y, Choi N, Cho IJ. Neural probe system for behavioral neuropharmacology by bi-directional wireless drug delivery and electrophysiology in socially interacting mice. Nat Commun 2022; 13:5521. [PMID: 36130965 PMCID: PMC9492903 DOI: 10.1038/s41467-022-33296-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Assessing the neurological and behavioral effects of drugs is important in developing pharmacological treatments, as well as understanding the mechanisms associated with neurological disorders. Herein, we present a miniaturized, wireless neural probe system with the capability of delivering drugs for the real-time investigation of the effects of the drugs on both behavioral and neural activities in socially interacting mice. We demonstrate wireless drug delivery and simultaneous monitoring of the resulting neural, behavioral changes, as well as the dose-dependent and repeatable responses to drugs. Furthermore, in pairs of mice, we use a food competition assay in which social interaction was modulated by the delivery of the drug, and the resulting changes in their neural activities are analyzed. During modulated food competition by drug injection, we observe changes in neural activity in mPFC region of a participating mouse over time. Our system may provide new opportunities for the development of studying the effects of drugs on behaviour and neural activity. Technologies for monitoring electrophysiological effects of drugs in behaving animals have limitations. Here the authors report a wireless neural probe system with drug delivery capability for real-time monitoring of drug effects.
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Affiliation(s)
- Yousang Yoon
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Hyogeun Shin
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Donghak Byun
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Jiwan Woo
- Research Animal Resource Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Yakdol Cho
- Research Animal Resource Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Il-Joo Cho
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, 02841, Republic of Korea.
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Ouellette N, Turschak E, Zhuang J. Co-registration of mouse cortical structures between in vivo and ex vivo images using tangential sectioning. STAR Protoc 2022; 3:101405. [PMID: 35620069 PMCID: PMC9127217 DOI: 10.1016/j.xpro.2022.101405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Co-registration of neuronal structures between in vivo and ex vivo imaging is necessary to study structure-function correspondence in the mammalian brain. Here we describe a protocol based on tangential sectioning of the mouse brain. This protocol aligns in vivo two-photon calcium imaging volumes with ex vivo confocal imaging volumes and registers the same cortical structures in both volumes. This approach allows detailed analysis of the corresponding function and structure of these entities. For complete details on the use and execution of this protocol, please refer to Zhuang et al. (2021).
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Affiliation(s)
| | | | - Jun Zhuang
- Allen Institute for Brain Science, Seattle, WA, USA
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Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex. eNeuro 2022; 9:ENEURO.0280-21.2021. [PMID: 35022186 PMCID: PMC8856714 DOI: 10.1523/eneuro.0280-21.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022] Open
Abstract
Despite significant progress in understanding neural coding, it remains unclear how the coordinated activity of large populations of neurons relates to what an observer actually perceives. Since neurophysiological differences must underlie differences among percepts, differentiation analysis—quantifying distinct patterns of neurophysiological activity—has been proposed as an “inside-out” approach that addresses this question. This methodology contrasts with “outside-in” approaches such as feature tuning and decoding analyses, which are defined in terms of extrinsic experimental variables. Here, we used two-photon calcium imaging in mice of both sexes to systematically survey stimulus-evoked neurophysiological differentiation (ND) in excitatory neuronal populations in layers (L)2/3, L4, and L5 across five visual cortical areas (primary, lateromedial, anterolateral, posteromedial, and anteromedial) in response to naturalistic and phase-scrambled movie stimuli. We find that unscrambled stimuli evoke greater ND than scrambled stimuli specifically in L2/3 of the anterolateral and anteromedial areas, and that this effect is modulated by arousal state and locomotion. By contrast, decoding performance was far above chance and did not vary substantially across areas and layers. Differentiation also differed within the unscrambled stimulus set, suggesting that differentiation analysis may be used to probe the ethological relevance of individual stimuli.
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