1
|
Desai NS, Zhong C, Kim R, Talmage DA, Role LW. A simple MATLAB toolbox for analyzing calcium imaging data in vitro and in vivo. J Neurosci Methods 2024; 409:110202. [PMID: 38906335 DOI: 10.1016/j.jneumeth.2024.110202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Fluorescence imaging of calcium dynamics in neuronal populations is powerful because it offers a way of relating the activity of individual cells to the broader population of nearby cells. The method's growth across neuroscience has particularly been driven by the introduction of sophisticated mathematical techniques related to motion correction, image registration, cell detection, spike estimation, and population characterization. However, for many researchers, making good use of these techniques has been difficult because they have been devised by different workers and impose differing - and sometimes stringent - technical requirements on those who seek to use them. NEW METHOD We have built a simple toolbox of analysis routines that encompass the complete workflow for analyzing calcium imaging data. The workflow begins with preprocessing of data, includes motion correction and longitudinal image registration, detects active cells using constrained non-negative matrix factorization, and offers multiple options for estimating spike times and characterizing population activity. The routines can be navigated through a simple graphical user interface. Although written in MATLAB, a standalone version for researchers who do not have access to MATLAB is included. RESULTS We have used the toolbox on two very different preparations: spontaneously active brain slices and microendoscopic imaging from deep structures in awake behaving mice. In both cases, the toolbox offered a seamless flow from raw data all the way through to prepared graphs. CONCLUSION The field of calcium imaging has benefited from the development of numerous innovative mathematical techniques. Here we offer a simple toolbox that allows ordinary researchers to fully exploit these techniques.
Collapse
Affiliation(s)
- Niraj S Desai
- Circuits, Synapses, and Molecular Signaling Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 90892, USA.
| | - Chongbo Zhong
- Circuits, Synapses, and Molecular Signaling Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 90892, USA
| | - Ronald Kim
- Genetics of Neuronal Signaling Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 90892, USA
| | - David A Talmage
- Genetics of Neuronal Signaling Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 90892, USA
| | - Lorna W Role
- Circuits, Synapses, and Molecular Signaling Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 90892, USA.
| |
Collapse
|
2
|
Bird AD, Cuntz H, Jedlicka P. Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus. PLoS Comput Biol 2024; 20:e1010706. [PMID: 38377108 PMCID: PMC10906873 DOI: 10.1371/journal.pcbi.1010706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/01/2024] [Accepted: 12/13/2023] [Indexed: 02/22/2024] Open
Abstract
Pattern separation is a valuable computational function performed by neuronal circuits, such as the dentate gyrus, where dissimilarity between inputs is increased, reducing noise and increasing the storage capacity of downstream networks. Pattern separation is studied from both in vivo experimental and computational perspectives and, a number of different measures (such as orthogonalisation, decorrelation, or spike train distance) have been applied to quantify the process of pattern separation. However, these are known to give conclusions that can differ qualitatively depending on the choice of measure and the parameters used to calculate it. We here demonstrate that arbitrarily increasing sparsity, a noticeable feature of dentate granule cell firing and one that is believed to be key to pattern separation, typically leads to improved classical measures for pattern separation even, inappropriately, up to the point where almost all information about the inputs is lost. Standard measures therefore both cannot differentiate between pattern separation and pattern destruction, and give results that may depend on arbitrary parameter choices. We propose that techniques from information theory, in particular mutual information, transfer entropy, and redundancy, should be applied to penalise the potential for lost information (often due to increased sparsity) that is neglected by existing measures. We compare five commonly-used measures of pattern separation with three novel techniques based on information theory, showing that the latter can be applied in a principled way and provide a robust and reliable measure for comparing the pattern separation performance of different neurons and networks. We demonstrate our new measures on detailed compartmental models of individual dentate granule cells and a dentate microcircuit, and show how structural changes associated with epilepsy affect pattern separation performance. We also demonstrate how our measures of pattern separation can predict pattern completion accuracy. Overall, our measures solve a widely acknowledged problem in assessing the pattern separation of neural circuits such as the dentate gyrus, as well as the cerebellum and mushroom body. Finally we provide a publicly available toolbox allowing for easy analysis of pattern separation in spike train ensembles.
Collapse
Affiliation(s)
- Alexander D. Bird
- Computer-Based Modelling in the field of 3R Animal Protection, ICAR3R, Faculty of Medicine, Justus Liebig University, Giessen, Germany
- Ernst Strüngmann Institute (ESI) for Neuroscience in cooperation with the Max Planck Society, Frankfurt-am-Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt-am-Main, Germany
- Translational Neuroscience Network Giessen, Germany
| | - Hermann Cuntz
- Ernst Strüngmann Institute (ESI) for Neuroscience in cooperation with the Max Planck Society, Frankfurt-am-Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt-am-Main, Germany
- Translational Neuroscience Network Giessen, Germany
| | - Peter Jedlicka
- Computer-Based Modelling in the field of 3R Animal Protection, ICAR3R, Faculty of Medicine, Justus Liebig University, Giessen, Germany
- Translational Neuroscience Network Giessen, Germany
| |
Collapse
|
3
|
Aoun A, Shetler O, Raghuraman R, Rodriguez GA, Hussaini SA. Beyond correlation: optimal transport metrics for characterizing representational stability and remapping in neurons encoding spatial memory. Front Cell Neurosci 2024; 17:1273283. [PMID: 38303974 PMCID: PMC10831886 DOI: 10.3389/fncel.2023.1273283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction Spatial representations in the entorhinal cortex (EC) and hippocampus (HPC) are fundamental to cognitive functions like navigation and memory. These representations, embodied in spatial field maps, dynamically remap in response to environmental changes. However, current methods, such as Pearson's correlation coefficient, struggle to capture the complexity of these remapping events, especially when fields do not overlap, or transformations are non-linear. This limitation hinders our understanding and quantification of remapping, a key aspect of spatial memory function. Methods We propose a family of metrics based on the Earth Mover's Distance (EMD) as a versatile framework for characterizing remapping. Results The EMD provides a granular, noise-resistant, and rate-robust description of remapping. This approach enables the identification of specific cell types and the characterization of remapping in various scenarios, including disease models. Furthermore, the EMD's properties can be manipulated to identify spatially tuned cell types and to explore remapping as it relates to alternate information forms such as spatiotemporal coding. Discussion We present a feasible, lightweight approach that complements traditional methods. Our findings underscore the potential of the EMD as a powerful tool for enhancing our understanding of remapping in the brain and its implications for spatial navigation, memory studies and beyond.
Collapse
Affiliation(s)
- Andrew Aoun
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Oliver Shetler
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Radha Raghuraman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Gustavo A. Rodriguez
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - S. Abid Hussaini
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| |
Collapse
|
4
|
Aoun A, Shetler O, Raghuraman R, Rodriguez GA, Hussaini SA. Beyond Correlation: Optimal Transport Metrics For Characterizing Representational Stability and Remapping in Neurons Encoding Spatial Memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548592. [PMID: 37503011 PMCID: PMC10369988 DOI: 10.1101/2023.07.11.548592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Spatial representations in the entorhinal cortex (EC) and hippocampus (HPC) are fundamental to cognitive functions like navigation and memory. These representations, embodied in spatial field maps, dynamically remap in response to environmental changes. However, current methods, such as Pearson's correlation coefficient, struggle to capture the complexity of these remapping events, especially when fields do not overlap, or transformations are non-linear. This limitation hinders our understanding and quantification of remapping, a key aspect of spatial memory function. To address this, we propose a family of metrics based on the Earth Mover's Distance (EMD) as a versatile framework for characterizing remapping. Applied to both normalized and unnormalized distributions, the EMD provides a granular, noise-resistant, and rate-robust description of remapping. This approach enables the identification of specific cell types and the characterization of remapping in various scenarios, including disease models. Furthermore, the EMD's properties can be manipulated to identify spatially tuned cell types and to explore remapping as it relates to alternate information forms such as spatiotemporal coding. By employing approximations of the EMD, we present a feasible, lightweight approach that complements traditional methods. Our findings underscore the potential of the EMD as a powerful tool for enhancing our understanding of remapping in the brain and its implications for spatial navigation, memory studies and beyond.
Collapse
Affiliation(s)
- Andrew Aoun
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Co-first author
| | - Oliver Shetler
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Co-first author
| | - Radha Raghuraman
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Gustavo A. Rodriguez
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - S. Abid Hussaini
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| |
Collapse
|
5
|
Witter J, Houghton C. Estimating Mutual Information for Spike Trains: A Bird Song Example. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1413. [PMID: 37895534 PMCID: PMC10606342 DOI: 10.3390/e25101413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023]
Abstract
Zebra finches are a model animal used in the study of audition. They are adept at recognizing zebra finch songs, and the neural pathway involved in song recognition is well studied. Here, this example is used to illustrate the estimation of mutual information between stimuli and responses using a Kozachenko-Leonenko estimator. The challenge in calculating mutual information for spike trains is that there are no obvious coordinates for the data. The Kozachenko-Leonenko estimator does not require coordinates; it relies only on the distance between data points. In the case of bird songs, estimating the mutual information demonstrates that the information content of spiking does not diminish as the song progresses.
Collapse
Affiliation(s)
- Jake Witter
- Faculty of Engineering, University of Bristol, Bristol BS8 1TR, UK;
| | | |
Collapse
|
6
|
Sotomayor-Gómez B, Battaglia FP, Vinck M. SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns. PLoS Comput Biol 2023; 19:e1011335. [PMID: 37523401 PMCID: PMC10414626 DOI: 10.1371/journal.pcbi.1011335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/10/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023] Open
Abstract
Neural coding and memory formation depend on temporal spiking sequences that span high-dimensional neural ensembles. The unsupervised discovery and characterization of these spiking sequences requires a suitable dissimilarity measure to spiking patterns, which can then be used for clustering and decoding. Here, we present a new dissimilarity measure based on optimal transport theory called SpikeShip, which compares multi-neuron spiking patterns based on all the relative spike-timing relationships among neurons. SpikeShip computes the optimal transport cost to make all the relative spike-timing relationships (across neurons) identical between two spiking patterns. We show that this transport cost can be decomposed into a temporal rigid translation term, which captures global latency shifts, and a vector of neuron-specific transport flows, which reflect inter-neuronal spike timing differences. SpikeShip can be effectively computed for high-dimensional neuronal ensembles, has a low (linear) computational cost that has the same order as the spike count, and is sensitive to higher-order correlations. Furthermore, SpikeShip is binless, can handle any form of spike time distributions, is not affected by firing rate fluctuations, can detect patterns with a low signal-to-noise ratio, and can be effectively combined with a sliding window approach. We compare the advantages and differences between SpikeShip and other measures like SPIKE and Victor-Purpura distance. We applied SpikeShip to large-scale Neuropixel recordings during spontaneous activity and visual encoding. We show that high-dimensional spiking sequences detected via SpikeShip reliably distinguish between different natural images and different behavioral states. These spiking sequences carried complementary information to conventional firing rate codes. SpikeShip opens new avenues for studying neural coding and memory consolidation by rapid and unsupervised detection of temporal spiking patterns in high-dimensional neural ensembles.
Collapse
Affiliation(s)
- Boris Sotomayor-Gómez
- Donders Centre for Neuroscience, Department of Neurophysics, Radboud University Nijmegen, Nijmegen, Netherlands
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, Frankfurt, Germany
| | - Francesco P. Battaglia
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Martin Vinck
- Donders Centre for Neuroscience, Department of Neurophysics, Radboud University Nijmegen, Nijmegen, Netherlands
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, Frankfurt, Germany
| |
Collapse
|
7
|
Lam D, Sebastian A, Bogguri C, Hum NR, Ladd A, Cadena J, Valdez CA, Fischer NO, Loots GG, Enright HA. Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures. FRONTIERS IN TOXICOLOGY 2022; 4:983415. [PMID: 36032789 PMCID: PMC9403314 DOI: 10.3389/ftox.2022.983415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Fentanyl is one of the most common opioid analgesics administered to patients undergoing surgery or for chronic pain management. While the side effects of chronic fentanyl abuse are recognized (e.g., addiction, tolerance, impairment of cognitive functions, and inhibit nociception, arousal, and respiration), it remains poorly understood what and how changes in brain activity from chronic fentanyl use influences the respective behavioral outcome. Here, we examined the functional and molecular changes to cortical neural network activity following sub-chronic exposure to two fentanyl concentrations, a low (0.01 μM) and high (10 μM) dose. Primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte precursor cells, were seeded in wells on either a 6-well multi-electrode array (MEA, for electrophysiology) or a 96-well tissue culture plate (for serial endpoint bulk RNA sequencing analysis). Once networks matured (at 28 days in vitro), co-cultures were treated with 0.01 or 10 μM of fentanyl for 4 days and monitored daily. Only high dose exposure to fentanyl resulted in a decline in features of spiking and bursting activity as early as 30 min post-exposure and sustained for 4 days in cultures. Transcriptomic analysis of the complex cultures after 4 days of fentanyl exposure revealed that both the low and high dose induced gene expression changes involved in synaptic transmission, inflammation, and organization of the extracellular matrix. Collectively, the findings of this in vitro study suggest that while neuroadaptive changes to neural network activity at a systems level was detected only at the high dose of fentanyl, transcriptomic changes were also detected at the low dose conditions, suggesting that fentanyl rapidly elicits changes in plasticity.
Collapse
Affiliation(s)
- Doris Lam
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Aimy Sebastian
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Chandrakumar Bogguri
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Nicholas R. Hum
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Alexander Ladd
- Computational Engineering Division, Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jose Cadena
- Computational Engineering Division, Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Carlos A. Valdez
- Nuclear and Chemical Sciences Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Nicholas O. Fischer
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Gabriela G. Loots
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Heather A. Enright
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
- *Correspondence: Heather A. Enright,
| |
Collapse
|