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

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.

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

10.1101/2021.07.15.452555 ◽

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.

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

10.1101/252205 ◽

2018 ◽

Cited By ~ 1

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.

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Implementation of a Six-Layer Smart Factory Architecture with Special Focus on Transdisciplinary Engineering Education

Sensors ◽

10.3390/s21092944 ◽

2021 ◽

Vol 21 (9) ◽

pp. 2944

Author(s):

Benjamin James Ralph ◽

Marcel Sorger ◽

Benjamin Schödinger ◽

Hans-Jörg Schmölzer ◽

Karin Hartl ◽

...

Keyword(s):

Open Source ◽

User Interfaces ◽

Industrial Revolution ◽

Low Cost ◽

Material Behavior ◽

Sensor Data ◽

Management Tool ◽

Special Focus ◽

Programming Environments ◽

Metal Processing

Smart factories are an integral element of the manufacturing infrastructure in the context of the fourth industrial revolution. Nevertheless, there is frequently a deficiency of adequate training facilities for future engineering experts in the academic environment. For this reason, this paper describes the development and implementation of two different layer architectures for the metal processing environment. The first architecture is based on low-cost but resilient devices, allowing interested parties to work with mostly open-source interfaces and standard back-end programming environments. Additionally, one proprietary and two open-source graphical user interfaces (GUIs) were developed. Those interfaces can be adapted front-end as well as back-end, ensuring a holistic comprehension of their capabilities and limits. As a result, a six-layer architecture, from digitization to an interactive project management tool, was designed and implemented in the practical workflow at the academic institution. To take the complexity of thermo-mechanical processing in the metal processing field into account, an alternative layer, connected with the thermo-mechanical treatment simulator Gleeble 3800, was designed. This framework is capable of transferring sensor data with high frequency, enabling data collection for the numerical simulation of complex material behavior under high temperature processing. Finally, the possibility of connecting both systems by using open-source software packages is demonstrated.

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In vivo fiber photometry of neural activity in response to optogenetically manipulated inputs in freely moving mice

Journal of Innovative Optical Health Sciences ◽

10.1142/s1793545817430015 ◽

2017 ◽

Vol 10 (05) ◽

pp. 1743001 ◽

Cited By ~ 6

Author(s):

Liang Li ◽

Yajie Tang ◽

Leqiang Sun ◽

Khaista Rahman ◽

Kai Huang ◽

...

Keyword(s):

Neuronal Activity ◽

Low Cost ◽

Functional Study ◽

V1 Neurons ◽

Dynamics Of Population ◽

Lateral Posterior ◽

Freely Moving ◽

Final Confirmation ◽

Detailed Protocol

In vivo fiber photometry is a powerful technique to analyze the dynamics of population neurons during functional study of neuroscience. Here, we introduced a detailed protocol for fiber photometry-based calcium recording in freely moving mice, covering from virus injection, fiber stub insertion, optogenetical stimulation to data procurement and analysis. Furthermore, we applied this protocol to explore neuronal activity of mice lateral-posterior (LP) thalamic nucleus in response to optogenetical stimulation of primary visual cortex (V1) neurons, and explore axon clusters activity of optogenetically evoked V1 neurons. Final confirmation of virus-based protein expression in V1 and precise fiber insertion indicated that the surgery procedure of this protocol is reliable for functional calcium recording. The scripts for data analysis and some tips in our protocol are provided in details. Together, this protocol is simple, low-cost, and effective for neuronal activity detection by fiber photometry, which will help neuroscience researchers to carry out functional and behavioral study in vivo.

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An easy-to-assemble, robust, and lightweight drive implant for chronic tetrode recordings in freely moving animals

10.1101/746651 ◽

2019 ◽

Author(s):

Jakob Voigts ◽

Jonathan P. Newman ◽

Matthew A. Wilson ◽

Mark T. Harnett

Keyword(s):

Ease Of Use ◽

Gold Standard Method ◽

Tree Shrews ◽

New Class ◽

Low Weight ◽

Build Time ◽

Freely Behaving ◽

Freely Moving ◽

Data Yield ◽

Tetrode Recordings

AbstractTetrode arrays are the gold-standard method for neuronal recordings in many studies with behaving animals, especially for deep structures and chronic recordings. Here we outline an improved drive design for use in freely behaving animals. Our design makes use of recently developed technologies to reduce the complexity and build time of the drive while maintaining a low weight. The design also presents an improvement over many existing designs in terms of robustness and ease of use. We describe two variants: a 16 tetrode implant weighing ∼2 g for mice, bats, tree shrews and similar animals, and a 64 tetrode implant weighing ∼16 g for rats, and similar animals.These designs were co-developed and optimized alongside a new class of drive-mounted feature-rich amplifier boards with ultra-thin RF tethers, as described in an upcoming paper (Newman, Zhang et al., in prep). This design significantly improves the data yield of chronic electrophysiology experiments.

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The DMCdrive: practical 3D-printable micro-drive system for reliable chronic multi-tetrode recording and optogenetic application in freely behaving rodents

10.1101/2020.04.24.059394 ◽

2020 ◽

Author(s):

Hoseok Kim ◽

Hans Sperup Brünner ◽

Marie Carlén

Keyword(s):

Low Cost ◽

Network Activity ◽

Electrophysiological Recording ◽

Electrophysiological Recordings ◽

Build Time ◽

Cell Type Specific ◽

Freely Behaving ◽

Freely Moving ◽

Electrophysiological Methods

AbstractElectrophysiological recording and optogenetic control of neuronal activity in behaving animals have been integral to the elucidation of how neurons and circuits modulate network activity in the encoding and causation of behavior. However, most current electrophysiological methods require substantial economical investments and prior expertise. Further, the inclusion of optogenetics with electrophysiological recordings in freely moving animals remains a general challenge. Expansion of the technological repertoire across laboratories, research institutes, and countries, demands open access to high-quality devices that can be built with little or no prior expertise from easily accessible parts of low cost. We here present a very affordable, truly easy-to-assemble micro-drive for electrophysiology in combination with optogenetics in freely moving mice and rats. The DMCdrive is particularly suited for reliable long-term recordings of neurons and network activities, and simplify optical tagging and manipulation of neurons in the recorded brain region. The highly functional and practical drive design has been optimized for accurate tetrode movement in brain tissue, and remarkably reduced build time. We provide a complete overview of the drive design, its assembly and use, and proof-of-principle demonstration of long-term recordings paired with cell-type-specific optogenetic manipulations in the prefrontal cortex (PFC) of freely moving transgenic mice and rats.

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Methods for Detecting PER2:LUCIFERASE Bioluminescence Rhythms in Freely Moving Mice

Journal of Biological Rhythms ◽

10.1177/07487304211062829 ◽

2021 ◽

pp. 074873042110628

Author(s):

Blanca Martin-Burgos ◽

Wanqi Wang ◽

Ivana William ◽

Selma Tir ◽

Innus Mohammad ◽

...

Keyword(s):

Gene Expression ◽

Circadian Rhythms ◽

Background Subtraction ◽

Room Temperature ◽

Small Difference ◽

Peripheral Clocks ◽

Freely Behaving ◽

Freely Moving ◽

Pharmacological Manipulations

Circadian rhythms are driven by daily oscillations of gene expression. An important tool for studying cellular and tissue circadian rhythms is the use of a gene reporter, such as bioluminescence from the reporter gene luciferase controlled by a rhythmically expressed gene of interest. Here we describe methods that allow measurement of circadian bioluminescence from a freely moving mouse housed in a standard cage. Using a LumiCycle In Vivo (Actimetrics), we determined conditions that allow detection of circadian rhythms of bioluminescence from the PER2 reporter, PER2::LUC, in freely behaving mice. The LumiCycle In Vivo applies a background subtraction that corrects for effects of room temperature on photomultiplier tube (PMT) output. We tested delivery of d-luciferin via a subcutaneous minipump and in the drinking water. We demonstrate spikes in bioluminescence associated with drinking bouts. Further, we demonstrate that a synthetic luciferase substrate, CycLuc1, can support circadian rhythms of bioluminescence, even when delivered at a lower concentration than d-luciferin, and can support longer-term studies. A small difference in phase of the PER2::LUC bioluminescence rhythms, with females phase leading males, can be detected with this technique. We share our analysis scripts and suggestions for further improvements in this method. This approach will be straightforward to apply to mice with tissue-specific reporters, allowing insights into responses of specific peripheral clocks to perturbations such as environmental or pharmacological manipulations.

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A low cost, open source Turbidostat design for in-vivo control experiments in Synthetic Biology

10.1101/617423 ◽

2019 ◽

Author(s):

Agostino Guarino ◽

Barbara Shannon ◽

Lucia Marucci ◽

Claire Grierson ◽

Nigel Savery ◽

...

Keyword(s):

Synthetic Biology ◽

Continuous Culture ◽

Open Source ◽

Optical Density ◽

Low Cost ◽

Control Design ◽

Engineered Systems

AbstractTo characterise the dynamics of new engineered systems in Synthetic biology, continuous culture platforms are required. In this paper, after a brief review of the existing machines present in literature, we describe the design and the implementation of a new flexible and low cost turbidostat for in-vivo control experiments. Then, the results of a 3 hours long experiment of control of the Optical Density is reported. Since the foundation of our design is flexibility, in this work we also discuss some possible extensions of our design, with particular attention to their application to validate in-vivo multicellular control design.

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Relationship between in vivo, in situ and in vitro techniques for evaluation of tropical forages in Brazil

Proceedings of the British Society of Animal Science ◽

10.1017/s1752756200007973 ◽

2002 ◽

Vol 2002 ◽

pp. 141-141

Author(s):

Ives C.S. Bueno ◽

Sergio L.S. Cabral Filho ◽

Liliana L. Oetting ◽

Mariana C. Machado ◽

Sarita P. Gobbo ◽

...

Keyword(s):

Low Cost ◽

Gas Production ◽

Ease Of Use ◽

In Vitro Techniques ◽

Evaluation Systems ◽

Similar Information ◽

Tropical Forages

In vivo experiments are the preferred method for ruminant feed evaluation, but they are very expensive, laborious and time-consuming. In situ and in vitro techniques are commonly used as a routine all over the world as a predictor of in vivo results. In situ assays have been the basis of many feed evaluation systems due to its ease of use and low cost. In vitro techniques, such as gas production, give an opportunity to get similar information plus a better description of fermentative kinetics. The aim of this work was to compare data obtained from in vivo, in vitro and in situ assays for the evaluation of three tropical forages used in ruminant nutrition in Brazil.

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