scholarly journals A compact head-mounted endoscope for in vivo calcium imaging in freely-behaving mice

2018 ◽  
Author(s):  
Alexander D. Jacob ◽  
Adam I. Ramsaran ◽  
Andrew J. Mocle ◽  
Lina M. Tran ◽  
Chen Yan ◽  
...  
Keyword(s):  
Open Source ◽  
Calcium Imaging ◽  
Low Cost ◽  
Population Level ◽  
Calcium Transients ◽  
Promising Tool ◽  
Calcium Indicator ◽  
Neuroscience Research ◽  
Freely Behaving

AbstractMiniaturized fluorescence microscopes for imaging calcium transients are a promising tool for investigating the relationship between behaviour and population-level neuronal activity in rodents. However, commercially available miniature microscopes may be costly, and, because they are closed-source, may not be easily modified based on particular experimental requirements. Here, we describe how to build and use a low-cost compact head-mounted endoscope (CHEndoscope) system for in vivo calcium imaging. The CHEndoscope uses an implanted gradient index (GRIN) lens along with the genetically encoded calcium indicator GCaMP6 to image calcium transients from hundreds of neurons simultaneously in awake behaving mice. This system is affordable, open-source, and flexible, permitting modification depending on the particular experiment. This Unit describes in detail the assembly, surgical implantation, data collection, and processing of calcium signals using the CHEndoscope system. The aim of this open framework model is to provide an accessible set of miniaturized calcium imaging tools for the neuroscience research community.Significance StatementThe ability to image calcium transients in awake, behaving rodents using miniature microscopes opens exciting and novel avenues for gaining insights into how information is encoded in neural circuits. The development of this tool has already had a significant impact on neuroscience research. The cost of commercial systems, however, may be prohibitive for many laboratories. Here, we describe an affordable, open-source compact head-mounted endoscope (CHEndoscope) system for performing in vivo calcium imaging in freely-behaving mice. CHEndoscopes may be manufactured by individual laboratories at relatively minor cost. Our hope is that greater availability of affordable, open-source tools (such as the one presented here) will accelerate the pace of discoveries in systems neuroscience.

scholarly journals Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

2015 ◽  
Vol 113 (8) ◽  
pp. E1074-E1081 ◽  
Author(s):  
Jeffrey P. Nguyen ◽  
Frederick B. Shipley ◽  
Ashley N. Linder ◽  
George S. Plummer ◽  
Mochi Liu ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Animal Behavior ◽  
Calcium Imaging ◽  
Large Scale ◽  
Calcium Transients ◽  
Whole Brain ◽  
Cellular Resolution ◽  
Calcium Indicator ◽  
Custom Software ◽  
Freely Behaving

The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. We present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal’s position, posture, and locomotion. This instrument provides whole-brain imaging with cellular resolution in an unrestrained and behaving animal. We use spinning-disk confocal microscopy to capture 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s at 6 head-volumes/s. A suite of three cameras monitor neuronal fluorescence and the animal’s position and orientation. Custom software tracks the 3D position of the animal’s head in real time and two feedback loops adjust a motorized stage and objective to keep the animal’s head within the field of view as the animal roams freely. We observe calcium transients from up to 77 neurons for over 4 min and correlate this activity with the animal’s behavior. We characterize noise in the system due to animal motion and show that, across worms, multiple neurons show significant correlations with modes of behavior corresponding to forward, backward, and turning locomotion.

scholarly journals GuPPy, a Python toolbox for the analysis of fiber photometry data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Venus N. Sherathiya ◽  
Michael D. Schaid ◽  
Jillian L. Seiler ◽  
Gabriela C. Lopez ◽  
Talia N. Lerner
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Low Cost ◽  
Ease Of Use ◽  
Analysis Tool ◽  
Freely Behaving ◽  
Freely Moving ◽  
Computing Platforms ◽  
Graphic User Interfaces

AbstractFiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be challenging for new users, especially those with a limited programming background. Here, we present Guided Photometry Analysis in Python (GuPPy), a free and open-source FP analysis tool. GuPPy is designed to operate across computing platforms and can accept data from a variety of FP data acquisition systems. The program presents users with a set of graphic user interfaces (GUIs) to load data and provide input parameters. Graphs are produced that can be easily exported for integration into scientific figures. As an open-source tool, GuPPy can be modified by users with knowledge of Python to fit their specific needs.

scholarly journals GuPPy, a Python toolbox for the analysis of fiber photometry data

2021 ◽  
Author(s):  
Venus N Sherathiya ◽  
Michael D Schaid ◽  
Jillian L Seiler ◽  
Gabriela C Lopez ◽  
Talia Lerner
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Low Cost ◽  
Ease Of Use ◽  
Analysis Tool ◽  
Development Environment ◽  
Freely Behaving ◽  
Freely Moving ◽  
Graphic User Interfaces

Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be a challenge for new users, especially those with a limited programming background. Here, we present Guided Photometry Analysis in Python (GuPPy), a free and open-source FP analysis tool. GuPPy is provided as a Jupyter notebook, a well-commented interactive development environment (IDE) designed to operate across platforms. GuPPy presents the user with a set of graphic user interfaces (GUIs) to load data and provide input parameters. Graphs produced by GuPPy can be exported into various image formats for integration into scientific figures. As an open-source tool, GuPPy can be modified by users with knowledge of Python to fit their specific needs.

scholarly journals A Compact Head-Mounted Endoscope for In Vivo Calcium Imaging in Freely Behaving Mice

2018 ◽  
Vol 84 (1) ◽  
pp. e51 ◽  
Author(s):  
Alexander D. Jacob ◽  
Adam I. Ramsaran ◽  
Andrew J. Mocle ◽  
Lina M. Tran ◽  
Chen Yan ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Freely Behaving ◽  
In Vivo Calcium Imaging

scholarly journals μECoG Recordings Through a Thinned Skull

2019 ◽  
Author(s):  
Sarah K. Brodnick ◽  
Jared P. Ness ◽  
Thomas J. Richner ◽  
Sanitta Thongpang ◽  
Joseph Novello ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Neural Signals ◽  
Electrophysiological Recordings ◽  
Neuroscience Research ◽  
Optically Transparent ◽  
Chronic Study ◽  
Multiple Species ◽  
First Time ◽  
Stimulation Of

AbstractThe studies described in this paper for the first time characterize the acute and chronic performance of optically transparent thin-film µECoG grids implanted on a thinned skull as both an electrophysiological complement to existing thinned skull preparation for optical recordings/manipulations, and a less invasive alternative to epidural or subdurally placed µECoG arrays. In a longitudinal chronic study, µECoG grids placed on top of a thinned skull maintain impedances comparable to epidurally placed µECoG grids that are stable for periods of at least one month. Optogenetic activation of cortex is also reliably demonstrated through the optically transparent ECoG grids acutely placed on the thinned skull. Finally, spatially distinct electrophysiological recordings were evident on µECoG electrodes placed on a thinned skull separated by 500-750µm, as assessed by stimulation evoked responses using optogenetic activation of cortex as well as invasive and epidermal stimulation of the sciatic and median nerve at chronic time points. Neural signals were collected through a thinned skull in multiple species, demonstrating potential utility in neuroscience research applications such as in vivo imaging, optogenetics, calcium imaging, and neurovascular coupling.

scholarly journals In vivo calcium imaging of CA3 pyramidal neuron populations in adult mouse hippocampus

2021 ◽  
Author(s):  
Gwendolin Schoenfeld ◽  
Stefano Carta ◽  
Peter Rupprecht ◽  
Aslı Ayaz ◽  
Fritjof Helmchen
Keyword(s):  
Calcium Imaging ◽  
Action Potentials ◽  
Pyramidal Neurons ◽  
Population Level ◽  
Calcium Transients ◽  
Population Activity ◽  
Brain Functions ◽  
State Dependent ◽  
Multiple Imaging ◽  
Ca3 Pyramidal Neurons

Neuronal population activity in the hippocampal CA3 subfield is implicated in cognitive brain functions such as memory processing and spatial navigation. However, because of its deep location in the brain, the CA3 area has been difficult to target with modern calcium imaging approaches. Here, we achieved chronic two-photon calcium imaging of CA3 pyramidal neurons with the red fluorescent calcium indicator R-CaMP1.07 in anesthetized and awake mice. We characterize CA3 neuronal activity at both the single-cell and population level and assess its stability across multiple imaging days. During both anesthesia and wakefulness, nearly all CA3 pyramidal neurons displayed calcium transients. Most of the calcium transients were consistent with a high incidence of bursts of action potentials, based on calibration measurements using simultaneous juxtacellular recordings and calcium imaging. In awake mice, we found state-dependent differences with striking large and prolonged calcium transients during locomotion. We estimate that trains of >30 action potentials over 3 s underlie these salient events. Their abundance in particular subsets of neurons was relatively stable across days. At the population level, we found that coactivity within the CA3 network was above chance level and that co-active neuron pairs maintained their correlated activity over days. Our results corroborate the notion of state-dependent spatiotemporal activity patterns in the recurrent network of CA3 and demonstrate that at least some features of population activity, namely coactivity of cell pairs and likelihood to engage in prolonged high activity, are maintained over days.

scholarly journals New and improved GRAB fluorescent sensors for monitoring dopaminergic activity in vivo

2020 ◽  
Author(s):  
Fangmiao Sun ◽  
Jingheng Zhou ◽  
Bing Dai ◽  
Tongrui Qian ◽  
Jianzhi Zeng ◽  
...  
Keyword(s):  
Critical Role ◽  
Brain Slices ◽  
Dopaminergic Activity ◽  
Gpcr Activation ◽  
Calcium Indicator ◽  
Freely Behaving ◽  
Green Fluorescent ◽  
Subcellular Resolution ◽  
Da Release

The monoamine neuromodulator dopamine (DA) plays a critical role in the brain, and the ability to directly measure dopaminergic activity is essential for understanding its physiological functions. We therefore developed the first red fluorescent GPCR-activation–based DA (GRABDA) sensors and optimized versions of green fluorescent GRABDA sensors following our previous studies. In response to extracellular DA, both the red and green GRABDA sensors have a large increase in fluorescence (ΔF/F0 values of 150% and 340%, respectively), with subcellular resolution, subsecond kinetics, and nanomolar to submicromolar affinity. Moreover, both the red and green GRABDA sensors readily resolve evoked DA release in mouse brain slices, detect compartmental DA release in live flies with single-cell resolution, and report optogenetically elicited nigrostriatal DA release as well as mesoaccumbens dopaminergic activity during sexual behavior in freely behaving mice. Importantly, co-expressing red GRABDA with either green GRABDA or the calcium indicator GCaMP6s provides a robust tool for simultaneously tracking neuronal activity and dopaminergic signaling in distinct circuits in vivo.

scholarly journals Soft subdermal implant capable of wireless battery charging and programmable controls for applications in optogenetics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Choong Yeon Kim ◽  
Min Jeong Ku ◽  
Raza Qazi ◽  
Hong Jae Nam ◽  
Jong Woo Park ◽  
...  
Keyword(s):  
Optical Fibers ◽  
Therapeutic Interventions ◽  
Full Potential ◽  
Wireless Power ◽  
Optoelectronic System ◽  
Neuroscience Research ◽  
Freely Behaving ◽  
Wireless Power Transfer System ◽  
Device Operation

AbstractOptogenetics is a powerful technique that allows target-specific spatiotemporal manipulation of neuronal activity for dissection of neural circuits and therapeutic interventions. Recent advances in wireless optogenetics technologies have enabled investigation of brain circuits in more natural conditions by releasing animals from tethered optical fibers. However, current wireless implants, which are largely based on battery-powered or battery-free designs, still limit the full potential of in vivo optogenetics in freely moving animals by requiring intermittent battery replacement or a special, bulky wireless power transfer system for continuous device operation, respectively. To address these limitations, here we present a wirelessly rechargeable, fully implantable, soft optoelectronic system that can be remotely and selectively controlled using a smartphone. Combining advantageous features of both battery-powered and battery-free designs, this device system enables seamless full implantation into animals, reliable ubiquitous operation, and intervention-free wireless charging, all of which are desired for chronic in vivo optogenetics. Successful demonstration of the unique capabilities of this device in freely behaving rats forecasts its broad and practical utilities in various neuroscience research and clinical applications.

scholarly journals LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging

2020 ◽  
Author(s):  
M.J.Y. Zimmermann ◽  
A.M. Chagas ◽  
P. Bartel ◽  
S. Pop ◽  
L.L. Prieto Godino ◽  
...  
Keyword(s):  
Fluorescence Detection ◽  
Colour Vision ◽  
Visual Stimulation ◽  
Low Cost ◽  
User Requirements ◽  
Light Stimulation ◽  
Led Driver ◽  
Two Photon ◽  
Neuroscience Research

AbstractTwo-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection. To overcome this limitation, we present a simple and low-cost electronic solution based on an ESP32 microcontroller and a TLC5947 LED driver to rapidly time-interleave stimulation and detection epochs during scans. Implemented for less than $100, our design can independently drive up to 24 arbitrary spectrum LEDs to meet user requirements. We demonstrate the utility of our stimulator for colour vision experiments on the in vivo tetrachromatic zebrafish retina and for optogenetic circuit mapping in Drosophila.https://github.com/BadenLab/LED-Zappelin

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