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Cepkenovic B, Friedland F, Noetzel E, Maybeck V, Offenhäusser A. Single-neuron mechanical perturbation evokes calcium plateaus that excite and modulate the network. Sci Rep 2023; 13:20669. [PMID: 38001109 PMCID: PMC10673841 DOI: 10.1038/s41598-023-47090-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Mechanical stimulation is a promising means to non-invasively excite and modulate neuronal networks with a high spatial resolution. Despite the thorough characterization of the initiation mechanism, whether or how mechanical responses disperse into non-target areas remains to be discovered. Our in vitro study demonstrates that a single-neuron deformation evokes responses that propagate to about a third of the untouched neighbors. The responses develop via calcium influx through mechanosensitive channels and regeneratively propagate through the neuronal ensemble via gap junctions. Although independent of action potentials and synapses, mechanical responses reliably evoke membrane depolarizations capable of inducing action potentials both in the target and neighbors. Finally, we show that mechanical stimulation transiently potentiates the responding assembly for further inputs, as both gain and excitability are transiently increased exclusively in neurons that respond to a neighbor's mechanical stimulation. The findings indicate a biological component affecting the spatial resolution of mechanostimulation and point to a cross-talk in broad-network mechanical stimulations. Since giga-seal formation in patch-clamp produces a similar mechanical stimulus on the neuron, our findings inform which neuroscientific questions could be reliably tackled with patch-clamp and what recovery post-gigaseal formation is necessary.
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Affiliation(s)
- Bogdana Cepkenovic
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße 1, 52428, Jülich, Germany
- RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
| | - Florian Friedland
- Institute of Biological Information Processing: Mechanobiology (IBI-2), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße 1, 52428, Jülich, Germany
| | - Erik Noetzel
- Institute of Biological Information Processing: Mechanobiology (IBI-2), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße 1, 52428, Jülich, Germany
| | - Vanessa Maybeck
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße 1, 52428, Jülich, Germany.
| | - Andreas Offenhäusser
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße 1, 52428, Jülich, Germany
- RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
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2
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Wysmolek PM, Kiessler FD, Salbaum KA, Shelton ER, Sonntag SM, Serwane F. A minimal-complexity light-sheet microscope maps network activity in 3D neuronal systems. Sci Rep 2022; 12:20420. [PMID: 36443413 PMCID: PMC9705530 DOI: 10.1038/s41598-022-24350-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022] Open
Abstract
In vitro systems mimicking brain regions, brain organoids, are revolutionizing the neuroscience field. However, characterization of their electrical activity has remained a challenge as it requires readout at millisecond timescale in 3D at single-neuron resolution. While custom-built microscopes used with genetically encoded sensors are now opening this door, a full 3D characterization of organoid neural activity has not been performed yet, limited by the combined complexity of the optical and the biological system. Here, we introduce an accessible minimalistic light-sheet microscope to the neuroscience community. Designed as an add-on to a standard inverted microscope it can be assembled within one day. In contrast to existing simplistic setups, our platform is suited to record volumetric calcium traces. We successfully extracted 4D calcium traces at high temporal resolution by using a lightweight piezo stage to allow for 5 Hz volumetric scanning combined with a processing pipeline for true 3D neuronal trace segmentation. As a proof of principle, we created a 3D connectivity map of a stem cell derived neuron spheroid by imaging its activity. Our fast, low complexity setup empowers researchers to study the formation of neuronal networks in vitro for fundamental and neurodegeneration research.
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Affiliation(s)
- Paulina M. Wysmolek
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Filippo D. Kiessler
- grid.5252.00000 0004 1936 973XFaculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katja A. Salbaum
- grid.5252.00000 0004 1936 973XFaculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany ,Graduate School of Systemic Neuroscience (GSN), Munich, Germany
| | - Elijah R. Shelton
- grid.5252.00000 0004 1936 973XFaculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Selina M. Sonntag
- grid.5252.00000 0004 1936 973XFaculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Friedhelm Serwane
- grid.5252.00000 0004 1936 973XFaculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany ,Graduate School of Systemic Neuroscience (GSN), Munich, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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3
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Cai Y, Wu J, Dai Q. Review on data analysis methods for mesoscale neural imaging in vivo. NEUROPHOTONICS 2022; 9:041407. [PMID: 35450225 PMCID: PMC9010663 DOI: 10.1117/1.nph.9.4.041407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Significance: Mesoscale neural imaging in vivo has gained extreme popularity in neuroscience for its capacity of recording large-scale neurons in action. Optical imaging with single-cell resolution and millimeter-level field of view in vivo has been providing an accumulated database of neuron-behavior correspondence. Meanwhile, optical detection of neuron signals is easily contaminated by noises, background, crosstalk, and motion artifacts, while neural-level signal processing and network-level coordinate are extremely complicated, leading to laborious and challenging signal processing demands. The existing data analysis procedure remains unstandardized, which could be daunting to neophytes or neuroscientists without computational background. Aim: We hope to provide a general data analysis pipeline of mesoscale neural imaging shared between imaging modalities and systems. Approach: We divide the pipeline into two main stages. The first stage focuses on extracting high-fidelity neural responses at single-cell level from raw images, including motion registration, image denoising, neuron segmentation, and signal extraction. The second stage focuses on data mining, including neural functional mapping, clustering, and brain-wide network deduction. Results: Here, we introduce the general pipeline of processing the mesoscale neural images. We explain the principles of these procedures and compare different approaches and their application scopes with detailed discussions about the shortcomings and remaining challenges. Conclusions: There are great challenges and opportunities brought by the large-scale mesoscale data, such as the balance between fidelity and efficiency, increasing computational load, and neural network interpretability. We believe that global circuits on single-neuron level will be more extensively explored in the future.
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Affiliation(s)
- Yeyi Cai
- Tsinghua University, Department of Automation, Beijing, China
| | - Jiamin Wu
- Tsinghua University, Department of Automation, Beijing, China
| | - Qionghai Dai
- Tsinghua University, Department of Automation, Beijing, China
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4
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Moroni M, Brondi M, Fellin T, Panzeri S. SmaRT2P: a software for generating and processing smart line recording trajectories for population two-photon calcium imaging. Brain Inform 2022; 9:18. [PMID: 35927517 PMCID: PMC9352634 DOI: 10.1186/s40708-022-00166-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or few action potentials when large number of neurons are imaged. We recently showed that implementing a smart line scanning approach using trajectories that optimally sample the regions of interest increases both the SNR fluorescence signals and the accuracy of single spike detection in population imaging in vivo. However, smart line scanning requires highly specialised software to design recording trajectories, interface with acquisition hardware, and efficiently process acquired data. Furthermore, smart line scanning needs optimized strategies to cope with movement artefacts and neuropil contamination. Here, we develop and validate SmaRT2P, an open-source, user-friendly and easy-to-interface Matlab-based software environment to perform optimized smart line scanning in two-photon calcium imaging experiments. SmaRT2P is designed to interface with popular acquisition software (e.g., ScanImage) and implements novel strategies to detect motion artefacts, estimate neuropil contamination, and minimize their impact on functional signals extracted from neuronal population imaging. SmaRT2P is structured in a modular way to allow flexibility in the processing pipeline, requiring minimal user intervention in parameter setting. The use of SmaRT2P for smart line scanning has the potential to facilitate the functional investigation of large neuronal populations with increased SNR and accuracy in detecting the discharge of single and few action potentials.
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Affiliation(s)
- Monica Moroni
- Neural Computation Laboratory, Center for Neuroscience and Cognitive Systems, UniTn, Istituto Italiano Di Tecnologia, 38068, Rovereto, Italy.
| | - Marco Brondi
- Optical Approaches to Brain Function Laboratory, Istituto Italiano Di Tecnologia, 16163, Genoa, Italy.,Department of Biomedical Sciences-UNIPD, Università Degli Studi Di Padova, 35121, Padua, Italy.,Padova Neuroscience Center (PNC), Università Degli Studi Di Padova, 35129, Padua, Italy
| | - Tommaso Fellin
- Optical Approaches to Brain Function Laboratory, Istituto Italiano Di Tecnologia, 16163, Genoa, Italy
| | - Stefano Panzeri
- Neural Computation Laboratory, Center for Neuroscience and Cognitive Systems, UniTn, Istituto Italiano Di Tecnologia, 38068, Rovereto, Italy. .,Department of Excellence for Neural Information Processing, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany.
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5
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Marolt U, Paradiž Leitgeb E, Pohorec V, Lipovšek S, Venglovecz V, Gál E, Ébert A, Menyhárt I, Potrč S, Gosak M, Dolenšek J, Stožer A. Calcium imaging in intact mouse acinar cells in acute pancreas tissue slices. PLoS One 2022; 17:e0268644. [PMID: 35657915 PMCID: PMC9165796 DOI: 10.1371/journal.pone.0268644] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
The physiology and pathophysiology of the exocrine pancreas are in close connection to changes in intra-cellular Ca2+ concentration. Most of our knowledge is based on in vitro experiments on acinar cells or acini enzymatically isolated from their surroundings, which can alter their structure, physiology, and limit our understanding. Due to these limitations, the acute pancreas tissue slice technique was introduced almost two decades ago as a complementary approach to assess the morphology and physiology of both the endocrine and exocrine pancreas in a more conserved in situ setting. In this study, we extend previous work to functional multicellular calcium imaging on acinar cells in tissue slices. The viability and morphological characteristics of acinar cells within the tissue slice were assessed using the LIVE/DEAD assay, transmission electron microscopy, and immunofluorescence imaging. The main aim of our study was to characterize the responses of acinar cells to stimulation with acetylcholine and compare them with responses to cerulein in pancreatic tissue slices, with special emphasis on inter-cellular and inter-acinar heterogeneity and coupling. To this end, calcium imaging was performed employing confocal microscopy during stimulation with a wide range of acetylcholine concentrations and selected concentrations of cerulein. We show that various calcium oscillation parameters depend monotonically on the stimulus concentration and that the activity is rather well synchronized within acini, but not between acini. The acute pancreas tissue slice represents a viable and reliable experimental approach for the evaluation of both intra- and inter-cellular signaling characteristics of acinar cell calcium dynamics. It can be utilized to assess many cells simultaneously with a high spatiotemporal resolution, thus providing an efficient and high-yield platform for future studies of normal acinar cell biology, pathophysiology, and screening pharmacological substances.
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Affiliation(s)
- Urška Marolt
- Clinical department for abdominal and general surgery, University Medical Centre Maribor, Maribor, Slovenia
- * E-mail: (UM); (JD); (AS)
| | - Eva Paradiž Leitgeb
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Viljem Pohorec
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Saška Lipovšek
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Viktória Venglovecz
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
| | - Eleonóra Gál
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
| | - Attila Ébert
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
| | - István Menyhárt
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
| | - Stojan Potrč
- Clinical department for abdominal and general surgery, University Medical Centre Maribor, Maribor, Slovenia
| | - Marko Gosak
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Jurij Dolenšek
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
- * E-mail: (UM); (JD); (AS)
| | - Andraž Stožer
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- * E-mail: (UM); (JD); (AS)
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6
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Laing BT, Siemian JN, Sarsfield S, Aponte Y. Fluorescence microendoscopy for in vivo deep-brain imaging of neuronal circuits. J Neurosci Methods 2021; 348:109015. [PMID: 33259847 PMCID: PMC8745022 DOI: 10.1016/j.jneumeth.2020.109015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022]
Abstract
Imaging neuronal activity in awake, behaving animals has become a groundbreaking method in neuroscience that has rapidly enhanced our understanding of how the brain works. In vivo microendoscopic imaging has enabled researchers to see inside the brains of experimental animals and thus has emerged as a technology fit to answer many experimental questions. By combining microendoscopy with cutting edge targeting strategies and sophisticated analysis tools, neuronal activity patterns that underlie changes in behavior and physiology can be identified. However, new users may find it challenging to understand the techniques and to leverage this technology to best suit their needs. Here we present a background and overview of the necessary components for performing in vivo optical calcium imaging and offer some detailed guidance for current recommended approaches.
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Affiliation(s)
- Brenton T Laing
- Neuronal Circuits and Behavior Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224-6823, USA
| | - Justin N Siemian
- Neuronal Circuits and Behavior Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224-6823, USA
| | - Sarah Sarsfield
- Neuronal Circuits and Behavior Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224-6823, USA
| | - Yeka Aponte
- Neuronal Circuits and Behavior Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224-6823, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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7
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Beed P, de Filippo R, Holman C, Johenning FW, Leibold C, Caputi A, Monyer H, Schmitz D. Layer 3 Pyramidal Cells in the Medial Entorhinal Cortex Orchestrate Up-Down States and Entrain the Deep Layers Differentially. Cell Rep 2020; 33:108470. [DOI: 10.1016/j.celrep.2020.108470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 06/26/2020] [Accepted: 11/10/2020] [Indexed: 01/27/2023] Open
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8
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Shah SI, Ong HL, Demuro A, Ullah G. PunctaSpecks: A tool for automated detection, tracking, and analysis of multiple types of fluorescently labeled biomolecules. Cell Calcium 2020; 89:102224. [PMID: 32502904 PMCID: PMC7343294 DOI: 10.1016/j.ceca.2020.102224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 01/21/2023]
Abstract
Recent advances in imaging technology and fluorescent probes have made it possible to gain information about the dynamics of subcellular processes at unprecedented spatiotemporal scales. Unfortunately, a lack of automated tools to efficiently process the resulting imaging data encoding fine details of the biological processes remains a major bottleneck in utilizing the full potential of these powerful experimental techniques. Here we present a computational tool, called PunctaSpecks, that can characterize fluorescence signals arising from a wide range of biological molecules under normal and pathological conditions. Among other things, the program can calculate the number, areas, life-times, and amplitudes of fluorescence signals arising from multiple sources, track diffusing fluorescence sources like moving mitochondria, and determine the overlap probability of two processes or organelles imaged using indicator dyes of different colors. We have tested PunctaSpecks on synthetic time-lapse movies containing mobile fluorescence objects of various sizes, mimicking the activity of biomolecules. The robustness of the software is tested by varying the level of noise along with random but known pattern of appearing, disappearing, and movement of these objects. Next, we use PunctaSpecks to characterize protein-protein interaction involved in store-operated Ca2+ entry through the formation and activation of plasma membrane-bound ORAI1 channel and endoplasmic reticulum membrane-bound stromal interaction molecule (STIM), the evolution of inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ signals from sub-micrometer size local events into global waves in human cortical neurons, and the activity of Alzheimer's disease-associated β amyloid pores in the plasma membrane. The tool can also be used to study other dynamical processes imaged through fluorescence molecules. The open source algorithm allows for extending the program to analyze more than two types of biomolecules visualized using markers of different colors.
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Affiliation(s)
| | - Hwei Ling Ong
- Secretory Physiology Section, NIDCR, NIH, Bethesda, MD, 20892,USA
| | - Angelo Demuro
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33647, USA.
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9
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Circuit-Specific Dendritic Development in the Piriform Cortex. eNeuro 2020; 7:ENEURO.0083-20.2020. [PMID: 32457067 PMCID: PMC7307633 DOI: 10.1523/eneuro.0083-20.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 11/21/2022] Open
Abstract
Dendritic geometry is largely determined during postnatal development and has a substantial impact on neural function. In sensory processing, postnatal development of the dendritic tree is affected by two dominant circuit motifs, ascending sensory feedforward inputs and descending and local recurrent connections. In the three-layered anterior piriform cortex (aPCx), neurons in the sublayers 2a and 2b display vertical segregation of these two circuit motifs. Here, we combined electrophysiology, detailed morphometry, and Ca2+ imaging in acute mouse brain slices and modeling to study circuit-specific aspects of dendritic development. We observed that determination of branching complexity, dendritic length increases, and pruning occurred in distinct developmental phases. Layer 2a and layer 2b neurons displayed developmental phase-specific differences between their apical and basal dendritic trees related to differences in circuit incorporation. We further identified functional candidate mechanisms for circuit-specific differences in postnatal dendritic growth in sublayers 2a and 2b at the mesoscale and microscale levels. Already in the first postnatal week, functional connectivity of layer 2a and layer 2b neurons during early spontaneous network activity scales with differences in basal dendritic growth. During the early critical period of sensory plasticity in the piriform cortex, our data are consistent with a model that proposes a role for dendritic NMDA-spikes in selecting branches for survival during developmental pruning in apical dendrites. The different stages of the morphologic and functional developmental pattern differences between layer 2a and layer 2b neurons demonstrate the complex interplay between dendritic development and circuit specificity.
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10
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Pnevmatikakis EA. Analysis pipelines for calcium imaging data. Curr Opin Neurobiol 2019; 55:15-21. [PMID: 30529147 DOI: 10.1016/j.conb.2018.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/11/2018] [Accepted: 11/19/2018] [Indexed: 11/26/2022]
Abstract
Calcium imaging is a popular tool among neuroscientists because of its capability to monitor in vivo large neural populations across weeks with single neuron and single spike resolution. Before any downstream analysis, the data needs to be pre-processed to extract the location and activity of the neurons and processes in the observed field of view. The ever increasing size of calcium imaging datasets necessitates scalable analysis pipelines that are reproducible and fully automated. This review focuses on recent methods for addressing the pre-processing problems that arise in calcium imaging data analysis, and available software tools for high throughput analysis pipelines.
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11
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Bar El Y, Kanner S, Barzilai A, Hanein Y. Calcium imaging, MEA recordings, and immunostaining images dataset of neuron-astrocyte networks in culture under the effect of norepinephrine. Gigascience 2019; 8:5244747. [PMID: 30544133 PMCID: PMC6351728 DOI: 10.1093/gigascience/giy161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022] Open
Abstract
Background Monitoring the activity and morphology of neuron-astrocyte networks in culture is a powerful tool for studying dynamics, structure, and communication in neuron-astrocyte networks independently or as a model of the sub-brain network. These cultures are known to produce stereotypical patterns of activity, e.g., highly synchronized network bursts resembling sleep or seizure states, thus it enables the exploration of behaviors that can relate to brain function and disease. High-resolution microscopy of calcium imaging combined with simultaneous electrical recording provides a comprehensive overview on the network's dynamics. This setup makes it possible to apply global perturbations of electrical and chemical stimulation on the cultures during the recording task and to record the effects on network activity on-line. Morphological changes in the cultures can be obtained to have a complete dataset for structure-function study of neuron-astrocyte networks in vitro. Findings The 4 TB of data presented here was recorded and imaged as part of an accompanying study looking at in vitro structure-function of neuron-astrocyte networks. Simultaneous optical (calcium imaging) and electrical (micro-electrode array) recordings lasted 5–12 minutes and included spontaneous activity recording, electrical and chemical stimulation of neuron-astrocyte, and isolated astrocyte cultures. The data include activity recordings of 58 different cultures, with 1–2 regions of interest recorded for each culture. Production procedures, experimental protocols, and reuse options are included. The data have been suitable to reveal changes in the activity and morphology of the cultures and enabled observation and analysis of neuron-astrocyte and isolated astrocyte culture behaviors under the applied perturbations. Conclusions Our dataset is sufficient to show significant changes in activity and morphology of neuron-astrocyte networks in culture under the applied stimulations. More than 100 recordings of 58 different cultures give insight of the observation's significance and led to conclusions about astrocyte activity and neuron-astrocyte network communication. Making it available here will allow others to test new tools for calcium imaging analysis and extracellular neuronal voltage recordings.
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Affiliation(s)
- Yasmin Bar El
- School of Physics and Astronomy, Tel-Aviv University, 30 Chaim Levanon street, Tel- Aviv, 6997801, Israel
| | - Sivan Kanner
- Department of Neurobiology, Faculty of Life Sciences, Tel-Aviv University, 30 Chaim Levanon street , Tel-Aviv, 6997801, Israel
| | - Ari Barzilai
- Department of Neurobiology, Faculty of Life Sciences, Tel-Aviv University, 30 Chaim Levanon street, Tel-Aviv, 6997801, Israel.,Sagol School of Neuroscience, Tel-Aviv University, 30 Chaim Levanon street, Tel-Aviv, 6997801, Israel
| | - Yael Hanein
- Sagol School of Neuroscience, Tel-Aviv University, 30 Chaim Levanon street, Tel-Aviv, 6997801, Israel.,School of Electrical Engineering, Tel-Aviv University, 30 Chaim Levanon street, Tel-Aviv, 6997801, Israel
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12
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SICT: automated detection and supervised inspection of fast Ca 2+ transients. Sci Rep 2018; 8:15523. [PMID: 30341397 PMCID: PMC6195629 DOI: 10.1038/s41598-018-33847-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
Recent advances in live Ca2+ imaging with increasing spatial and temporal resolution offer unprecedented opportunities, but also generate an unmet need for data processing. Here we developed SICT, a MATLAB program that automatically identifies rapid Ca2+ rises in time-lapse movies with low signal-to-noise ratios, using fluorescent indicators. A graphical user interface allows visual inspection of automatically detected events, reducing manual labour to less than 10% while maintaining quality control. The detection performance was tested using synthetic data with various signal-to-noise ratios. The event inspection phase was evaluated by four human observers. Reliability of the method was demonstrated in a direct comparison between manual and SICT-aided analysis. As a test case in cultured neurons, SICT detected an increase in frequency and duration of spontaneous Ca2+ transients in the presence of caffeine. This new method speeds up the analysis of elementary Ca2+ transients.
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