A modular, cost-effective, versatile, open-source operant box solution for long-term miniscope imaging, 3D tracking, and deep learning behavioral analysis

In this procedure we have included an open-source method for a customized operant chamber optimized for long-term miniature microscope (miniscope) recordings. •The miniscope box is designed to function with custom or typical med-associates style accessories (e.g., houselights, levers, etc.).•The majority of parts can be directly purchased which minimizes the need for skilled and time-consuming labor.•We include designs and estimated pricing for a single box but it is recommended to build these in larger batches to efficiently utilize bulk ordering of certain components.

Open-MAC: A low-cost open-source motorized commutator for electro- and opto-physiological recordings in freely moving rodents

In vivo electro- and optophysiology experiments in rodents reveal the neural mechanisms underlying behavior and brain disorders but mostly involve a cable connection between an implant in the animal and an external recording device. Standard tethers with thin cables or non-motorized commutators require constant monitoring and often manual interference to untwist the cable. Motorized commutators offer a solution, but those few that are commercially available are expensive and often not adapted to widely used connector standards of the open-source community like 12-channel SPI. Here we introduce an open-source motorized all-in-one commutator (Open-MAC): a low-cost (240-390 EUR), low-torque motorized commutator that can operate with minimal audible noise in a torque-based mode relying on dual magnetic Hall sensors. It further includes electronics to operate in a torque-free, online pose-estimation-based mode, with future developments. Operation is controlled by an onboard microcontroller (XIAO SAMD21) powered by a USB-C cable or DC power supply. The body and movable parts are 3D-printed. Different Open-MAC versions can support electrophysiology with up to 64 recording channels using the Open-Ephys / Intan^TM recording systems as well as miniature endoscope (miniscope) recordings using the UCLA Miniscope v3/4, and can host a fibre for optogenetic modulation.

Spatial coding defects of hippocampal neural ensemble calcium activities in the triple-transgenic Alzheimer's disease mouse model

Alzheimer’s disease (AD) causes progressive age-related defects in memory and cognitive function and has emerged as a major health and socio-economic concern in the US and worldwide. To develop effective therapeutic treatments for AD, we need to better understand the neural mechanisms by which AD causes memory loss and cognitive deficits. Here we examine large-scale hippocampal neural population calcium activities imaged at single cell resolution in a triple-transgenic Alzheimer’s disease mouse model (3xTg-AD) that presents both amyloid plaque and neurofibrillary pathological features along with age-related behavioral defects. To measure encoding of environmental location in hippocampal neural ensembles in the 3xTg-AD mice in vivo, we performed GCaMP6-based calcium imaging using head-mounted, miniature fluorescent microscopes (“miniscopes”) on freely moving animals. We compared hippocampal CA1 excitatory neural ensemble activities during open-field exploration and track-based route-running behaviors in age-matched AD and control mice at young (3–6.5 months old) and old (18–21 months old) ages. During open-field exploration, 3xTg-AD CA1 excitatory cells display significantly higher calcium activity rates compared with Non-Tg controls for both the young and old age groups, suggesting that in vivo enhanced neuronal calcium ensemble activity is a disease feature. CA1 neuronal populations of 3xTg-AD mice show lower spatial information scores compared with control mice. The spatial firing of CA1 neurons of old 3xTg-AD mice also displays higher sparsity and spatial coherence, indicating less place specificity for spatial representation. We find locomotor speed significantly modulates the amplitude of hippocampal neural calcium ensemble activities to a greater extent in 3xTg-AD mice during open field exploration. Our data offer new and comprehensive information about age-dependent neural circuit activity changes in this important AD mouse model and provide strong evidence that spatial coding defects in the neuronal population activities are associated with AD pathology and AD-related memory behavioral deficits.

Orexin neuron activity in mating mice - a pilot study

Mating behaviours affect hypothalamic orexin/hypocretin neurons and vice versa. However, activity of orexin neurons has not been recorded during mating before. We report an anecdotal dataset of freely-moving miniature microscope recordings of orexin neuron activity during mating behaviours, as well as an oral sexual encounter previously undocumented in mice. Across the orexin neuron population in the male, firing rates were maximally diverse during ejaculation, similarly diverse though weaker during intromission, and inverse to this during anterior thrusting. In the female mouse, orexin neurons tended to decrease firing during intromission after a transient increase. We provide this brief dataset for re-use, to enable further studies of these rare behaviours with challenging surgical preparations.

iHELMET: A 3D-printing solution for safe endoscopic Ca2+ recording in social neuroscience

BACKGROUND

In vivo calcium imaging using a microendoscope is a state-of-the-art technique to study the cellular activity inside the brain of freely moving animals such as mice or rats. A problem that can arise in social behaviour tests in rats, or similar size rodents, is that one animal interferes with or may even damage the miniature endoscopic camera attached to the second animal.

NEW METHOD

We outline an inexpensive, lightweight, 3D-printed protector (iHELMET) that surrounds but is not in physical contact with the camera, together with details of its design and construction.

RESULTS

Using a simple design, we demonstrate successful protection of the endoscope and recording in a social situation such as the social dominance tube test.

COMPARISON WITH EXISTING METHODS

The helmet's 3D-printed dimensions can be readily adjusted to work with various micro-endoscopes, which may be more difficult for the only other system of which we are aware.

CONCLUSIONS

In addition to camera protection, features of the design aid camera stability, helping to secure more optimal imaging of calcium transients in specific regions of interest during long recording sessions.

Calcium imaging in freely-moving mice during electrical stimulation of deep brain structures

After decades of study in humans and animal models, there remains a lack of consensus regarding how the action of electrical stimulation on neuronal and non-neuronal elements - e.g. neuropil, cell bodies, glial cells, etc. - leads to the therapeutic effects of neuromodulation therapies. To further our understanding of neuromodulation therapies, there is a critical need for novel methodological approaches using state-of-the-art neuroscience tools to study neuromodulation therapy in preclinical models of disease. In this manuscript we outline one such approach combining chronic behaving single-photon microendoscope recordings in a pathological mouse model with electrical stimulation of a common deep brain stimulation (DBS) target. We describe in detail the steps necessary to realize this approach, as well as discuss key considerations for extending this experimental paradigm to other DBS targets for different therapeutic indications. Additionally, we make recommendations from our experience on implementing and validating the required combination of procedures that includes: the induction of a pathological model (6-OHDA model of Parkinson's disease) through an injection procedure, the injection of the viral vector to induce GCaMP expression, the implantation of the GRIN lens and stimulation electrode, and the installation of a baseplate for mounting the microendoscope. We proactively identify unique data analysis confounds occurring due to the combination of electrical stimulation and optical recordings and outline an approach to address these confounds. In order to validate the technical feasibility of this unique combination of experimental methods, we present data to demonstrate that 1) despite the complex multifaceted surgical procedures, chronic optical recordings of hundreds of cells combined with stimulation is achievable over week long periods 2) this approach enables measurement of differences in DBS evoked neural activity between anesthetized and awake conditions and 3) this combination of techniques can be used to measure electrical stimulation induced changes in neural activity during behavior in a pathological mouse model. These findings are presented to underscore the feasibility and potential utility of minimally constrained optical recordings to elucidate the mechanisms of DBS therapies in animal models of disease.

Concussion increases CA1 activity during prolonged inactivity in a familiar environment

Although hippocampal damage plays a key role in impairments after concussion, differences in hippocampal information processing during recovery are unknown. Micro-endoscopic calcium imaging was performed before and after primary blast injury in freely behaving mice in two environments: their familiar home cage and a novel open field. Results show that after concussion CA1 activity increased in the familiar environment in which animals were awake and mostly immobile but was unaltered in a novel environment which the animals actively and constantly explored. As awake immobility parallels cognitive rest, a common treatment for patients, the results imply that prolonged cognitive rest may unwittingly impede concussion recovery.

Functional interrogation of neural circuits with virally transmitted optogenetic tools

The vertebrate brain comprises a plethora of cell types connected by intertwined pathways. Optogenetics enriches the neuroscientific tool set for disentangling these neuronal circuits in a manner which exceeds the spatio-temporal precision of previously existing techniques. Technically, optogenetics can be divided in three types of optical and genetic combinations: (1) it is primarily understood as the manipulation of the activity of genetically modified cells (typically neurons) with light, i.e. optical actuators. (2) A second combination refers to visualizing the activity of genetically modified cells (again typically neurons), i.e. optical sensors. (3) A completely different interpretation of optogenetics refers to the light activated expression of a genetically induced construct. Here, we focus on the first two types of optogenetics, i.e. the optical actuators and sensors in an attempt to give an overview into the topic. We first cover methods to express opsins into neurons and introduce strategies of targeting specific neuronal populations in different animal species. We then summarize combinations of optogenetics with behavioral read out and neuronal imaging. Finally, we give an overview of the current state-of-the-art and an outlook on future perspectives.

Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors

Confirming the direct link between neural circuit activity and animal behavior has been a principal aim of neuroscience. The genetically encoded calcium indicator (GECI), which binds to calcium ions and emits fluorescence visualizing intracellular calcium concentration, enables detection of in vivo neuronal firing activity. Various GECIs have been developed and can be chosen for diverse purposes. These GECI-based signals can be acquired by several tools including two-photon microscopy and microendoscopy for precise or wide imaging at cellular to synaptic levels. In addition, the images from GECI signals can be analyzed with open source codes including constrained non-negative matrix factorization for endoscopy data (CNMF_E) and miniscope 1-photon-based calcium imaging signal extraction pipeline (MIN1PIPE), and considering parameters of the imaged brain regions (e.g., diameter or shape of soma or the resolution of recorded images), the real-time activity of each cell can be acquired and linked with animal behaviors. As a result, GECI signal analysis can be a powerful tool for revealing the functions of neuronal circuits related to specific behaviors.

Intraductal biliary and pancreatic endoscopy: An expanding scope of possibility

Intraductal endoscopy describes the use of an endoscope to directly visualize the biliary and pancreatic ducts. For many years, technological challenges have made performing these procedures difficult. The “mother-baby” system and other various miniscopes have been developed, but routine use has been hampered due to complex setup, scope fragility and the time consuming, technically demanding nature of the procedure. Recently, the SpyGlass peroral cholangiopancreatoscopy system has shown early success at providing diagnostic information and therapeutic options. The clinical utility of intraductal endoscopy is broad. It allows better differentiation between benign and malignant processes by allowing direct visualization and targeted sampling of tissue. Therapeutic interventions, such as electrohydraulic lithotripsy (EHL), laser lithotripsy, photodynamic therapy, and argon plasma coagulation (APC), may also be performed as part of intraductal endoscopy. Intraductal endoscopy significantly increases the diagnostic and therapeutic yield of standard endoscopic retrograde cholangiography (ERCP), and as technology progresses, it is likely that its utilization will only increase. In this review of intraductal endoscopy, we describe in detail the various endoscopic platforms and their diagnostic and clinical applications.