scholarly journals Mesmerize: A highly versatile platform for calcium imaging analysis and creation of self-contained FAIR datasets

2019 ◽  
Author(s):  
Kushal Kolar ◽  
Daniel Dondorp ◽  
Marios Chatzigeorgiou
Keyword(s):  
Calcium Imaging ◽  
Signal Extraction ◽  
Graphical Interface ◽  
Imaging Analysis ◽  
C Elegans ◽  
Analysis Process ◽  
Visual Cortex Neurons ◽  
Mouse Visual Cortex ◽  
Analysis Platform ◽  
Scientific Questions

AbstractWe present an efficient and expandable calcium imaging analysis platform that encapsulates the entire analysis process from raw data to interactive e-figures. It provides a graphical interface to the latest analysis methods for pre-processing, and signal extraction. We demonstrate how Mesmerize can be applied to a broad range of scientific questions by using datasets ranging from the mouse visual cortex, neurons, epidermis and TLCs of the protochordate C. intestinalis, and C. elegans.

scholarly journals Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kushal Kolar ◽  
Daniel Dondorp ◽  
Jordi Cornelis Zwiggelaar ◽  
Jørgen Høyer ◽  
Marios Chatzigeorgiou
Keyword(s):  
Calcium Imaging ◽  
Imaging Data ◽  
Cellular Mechanisms ◽  
Analysis Process ◽  
Organization Analysis ◽  
Interactive Visualizations ◽  
Downstream Analysis ◽  
User Friendly ◽  
Analysis Platform ◽  
2D And 3D

AbstractCalcium imaging is an increasingly valuable technique for understanding neural circuits, neuroethology, and cellular mechanisms. The analysis of calcium imaging data presents challenges in image processing, data organization, analysis, and accessibility. Tools have been created to address these problems independently, however a comprehensive user-friendly package does not exist. Here we present Mesmerize, an efficient, expandable and user-friendly analysis platform, which uses a Findable, Accessible, Interoperable and Reproducible (FAIR) system to encapsulate the entire analysis process, from raw data to interactive visualizations for publication. Mesmerize provides a user-friendly graphical interface to state-of-the-art analysis methods for signal extraction & downstream analysis. We demonstrate the broad scientific scope of Mesmerize’s applications by analyzing neuronal datasets from mouse and a volumetric zebrafish dataset. We also applied contemporary time-series analysis techniques to analyze a novel dataset comprising neuronal, epidermal, and migratory mesenchymal cells of the protochordate Ciona intestinalis.

scholarly journals Calcium imaging of multiple neurons in freely behaving C. elegans

2012 ◽  
Vol 206 (1) ◽  
pp. 78-82 ◽  
Author(s):  
Maohua Zheng ◽  
Pengxiu Cao ◽  
Jiong Yang ◽  
X.Z. Shawn Xu ◽  
Zhaoyang Feng
Keyword(s):  
Calcium Imaging ◽  
C Elegans ◽  
Freely Behaving

scholarly journals Real-Time Neuron Detection and Neural Signal Extraction Platform for Miniature Calcium Imaging

2020 ◽  
Vol 14 ◽  
Author(s):  
Yaesop Lee ◽  
Jing Xie ◽  
Eungjoo Lee ◽  
Srijesh Sudarsanan ◽  
Da-Ting Lin ◽  
...  
Keyword(s):  
Real Time ◽  
Calcium Imaging ◽  
Signal Extraction ◽  
Neural Signal

scholarly journals Pan-neuronal screening in Caenorhabditis elegans reveals asymmetric dynamics of AWC neurons is critical for thermal avoidance behavior

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ippei Kotera ◽  
Nhat Anh Tran ◽  
Donald Fu ◽  
Jimmy HJ Kim ◽  
Jarlath Byrne Rodgers ◽  
...  
Keyword(s):  
Avoidance Behavior ◽  
Calcium Imaging ◽  
Functional Screening ◽  
Noxious Heat ◽  
Thermal Nociception ◽  
C Elegans ◽  
Low Efficiency ◽  
Behavioral Transition ◽  
Thermal Stimuli

Understanding neural functions inevitably involves arguments traversing multiple levels of hierarchy in biological systems. However, finding new components or mechanisms of such systems is extremely time-consuming due to the low efficiency of currently available functional screening techniques. To overcome such obstacles, we utilize pan-neuronal calcium imaging to broadly screen the activity of the C. elegans nervous system in response to thermal stimuli. A single pass of the screening procedure can identify much of the previously reported thermosensory circuitry as well as identify several unreported thermosensory neurons. Among the newly discovered neural functions, we investigated in detail the role of the AWCOFF neuron in thermal nociception. Combining functional calcium imaging and behavioral assays, we show that AWCOFF is essential for avoidance behavior following noxious heat stimulation by modifying the forward-to-reversal behavioral transition rate. We also show that the AWCOFF signals adapt to repeated noxious thermal stimuli and quantify the corresponding behavioral adaptation.

scholarly journals Emergent orientation selectivity from random networks in mouse visual cortex

2018 ◽  
Author(s):  
J.J. Pattadkal ◽  
G. Mato ◽  
C. van Vreeswijk ◽  
N. J. Priebe ◽  
D. Hansel
Keyword(s):  
Visual Cortex ◽  
Calcium Imaging ◽  
Receptive Fields ◽  
Orientation Selectivity ◽  
Random Networks ◽  
Two Dimensional ◽  
V1 Neurons ◽  
Mouse Visual Cortex ◽  
Whole Cell Recordings ◽  
Random Connectivity

SummaryWe study the connectivity principles underlying the emergence of orientation selectivity in primary visual cortex (V1) of mammals lacking an orientation map. We present a computational model in which random connectivity gives rise to orientation selectivity that matches experimental observations. It predicts that mouse V1 neurons should exhibit intricate receptive fields in the two-dimensional frequency domain, causing shift in orientation preferences with spatial frequency. We find evidence for these features in mouse V1 using calcium imaging and intracellular whole cell recordings.

scholarly journals Electrophysiological and Transcriptomic Features Reveal a Circular Taxonomy of Cortical Neurons

2021 ◽  
Vol 15 ◽  
Author(s):  
Alejandro Rodríguez-Collado ◽  
Cristina Rueda
Keyword(s):  
Cortical Neurons ◽  
Cell Types ◽  
Mammalian Brain ◽  
Neuronal Dynamics ◽  
Electrophysiological Signals ◽  
Visual Cortex Neurons ◽  
Line Level ◽  
Mouse Visual Cortex ◽  
Different Levels

The complete understanding of the mammalian brain requires exact knowledge of the function of each neuron subpopulation composing its parts. To achieve this goal, an exhaustive, precise, reproducible, and robust neuronal taxonomy should be defined. In this paper, a new circular taxonomy based on transcriptomic features and novel electrophysiological features is proposed. The approach is validated by analysing more than 1850 electrophysiological signals of different mouse visual cortex neurons proceeding from the Allen Cell Types database. The study is conducted on two different levels: neurons and their cell-type aggregation into Cre lines. At the neuronal level, electrophysiological features have been extracted with a promising model that has already proved its worth in neuronal dynamics. At the Cre line level, electrophysiological and transcriptomic features are joined on cell types with available genetic information. A taxonomy with a circular order is revealed by a simple transformation of the first two principal components that allow the characterization of the different Cre lines. Moreover, the proposed methodology locates other Cre lines in the taxonomy that do not have transcriptomic features available. Finally, the taxonomy is validated by Machine Learning methods which are able to discriminate the different neuron types with the proposed electrophysiological features.

scholarly journals Electrophysiological and Transcriptomic Features Reveal a Circular Taxonomy of Cortical Neurons

2021 ◽  
Author(s):  
Alejandro Rodríguez-Collado ◽  
Cristina Rueda
Keyword(s):  
Cortical Neurons ◽  
Cell Types ◽  
Mammalian Brain ◽  
Neuronal Dynamics ◽  
Electrophysiological Signals ◽  
Visual Cortex Neurons ◽  
Line Level ◽  
Mouse Visual Cortex ◽  
Different Levels

The complete understanding of the mammalian brain requires exact knowledge of the function of each of the neurons composing its parts. To achieve this goal, an exhaustive, precise, reproducible, and robust neuronal taxonomy should be defined. In this paper, a new circular taxonomy based on transcriptomic features and novel electrophysiological features is proposed. The approach is validated by analysing more than 1850 electrophysiological signals of different mouse visual cortex neurons proceeding from the Allen Cell Types Database. The study is conducted on two different levels: neurons and their cell-type aggregation into Cre Lines. At the neuronal level, electrophysiological features have been extracted with a promising model that has already proved its worth in neuronal dynamics. At the Cre Line level, electrophysiological and transcriptomic features are joined on cell types with available genetic information. A taxonomy with a circular order is revealed by a simple transformation of the first two principal components that allow the characterization of the different Cre Lines. Moreover, the proposed methodology locates other Cre Lines in the taxonomy that do not have transcriptomic features available. Finally, the taxonomy is validated by Machine Learning methods which are able to discriminate the different neuron types with the proposed electrophysiological features.

scholarly journals Player-Driven Video Analysis to Enhance Reflective Soccer Practice in Talent Development

2018 ◽  
Vol 8 (2) ◽  
pp. 29-43 ◽  
Author(s):  
Anders Hjort ◽  
Kristoffer Henriksen ◽  
Lars Elbæk
Keyword(s):  
Video Analysis ◽  
Role Models ◽  
Deliberate Practice ◽  
Reflective Learning ◽  
Soccer Players ◽  
Youth Soccer ◽  
Analysis Process ◽  
Analysis Platform ◽  
Analytical Platforms ◽  
Game Performance

In the present article, we investigate the introduction of a cloud-based video analysis platform called Player Universe (PU). Video analysis is not a new performance-enhancing element in sports, but PU is innovative in how it facilitates reflective learning. Video analysis is executed in the PU platform by involving the players in the analysis process, in the sense that they are encouraged to tag game actions in video-documented soccer matches. Following this, players can get virtual feedback from their coach. Findings show that PU can improve youth soccer players' reflection skills through consistent video analyses and tagging; coaches are important as role models and providers of feedback; and that the use of the platform primarily stimulated deliberate practice activities. PU can be seen as a source of inspiration for soccer players and clubs as to how analytical platforms can motivate and enhance reflective learning for better in-game performance.

scholarly journals Wedge prism approach for simultaneous multichannel microscopy

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hanna Cai ◽  
Yao L. Wang ◽  
Richard T. Wainner ◽  
Nicusor V. Iftimia ◽  
Christopher V. Gabel ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Axial Direction ◽  
C Elegans ◽  
Non Invasive ◽  
Image Postprocessing ◽  
Spread Function ◽  
Wedge Prism ◽  
User Friendly ◽  
Biology Research

AbstractMultichannel (multicolor) imaging has become a powerful technique in biology research for performing in vivo neuronal calcium imaging, colocalization of fluorescent labels, non-invasive pH measurement, and other procedures. We describe a novel add-on approach for simultaneous multichannel optical microscopy based on simple wedge prisms. Our device requires no alignment and is simple, robust, user-friendly, and less expensive than current commercial instruments based on switchable filters or dual-view strategies. Point spread function measurements and simulations in Zemax indicate a reduction in resolution in the direction orthogonal to the wedge interface and in the axial direction, without introducing aberration. These effects depend on the objective utilized and are most significant near the periphery of the field of view. We tested a two-channel device on C. elegans neurons in vivo and demonstrated comparable signals to a conventional dual-view instrument. We also tested a four-channel device on fixed chick embryo Brainbow samples and identified individual neurons by their spectra without extensive image postprocessing. Therefore, we believe that this technology has the potential for broad use in microscopy.

Fast-GBS v2.0: an analysis toolkit for genotyping-by-sequencing data

Genome ◽  
2020 ◽  
Vol 63 (11) ◽  
pp. 577-581
Author(s):  
Davoud Torkamaneh ◽  
Jérôme Laroche ◽  
François Belzile
Keyword(s):  
Data Analysis ◽  
Missing Data ◽  
Low Cost ◽  
Genotyping By Sequencing ◽  
Data Imputation ◽  
Sequencing Data ◽  
Missing Data Imputation ◽  
Analysis Process ◽  
Computational Resources ◽  
Analysis Platform

Genotyping-by-sequencing (GBS) is a rapid, flexible, low-cost, and robust genotyping method that simultaneously discovers variants and calls genotypes within a broad range of samples. These characteristics make GBS an excellent tool for many applications and research questions from conservation biology to functional genomics in both model and non-model species. Continued improvement of GBS relies on a more comprehensive understanding of data analysis, development of fast and efficient bioinformatics pipelines, accurate missing data imputation, and active post-release support. Here, we present the second generation of Fast-GBS (v2.0) that offers several new options (e.g., processing paired-end reads and imputation of missing data) and features (e.g., summary statistics of genotypes) to improve the GBS data analysis process. The performance assessment analysis showed that Fast-GBS v2.0 outperformed other available analytical pipelines, such as GBS-SNP-CROP and Gb-eaSy. Fast-GBS v2.0 provides an analysis platform that can be run with different types of sequencing data, modest computational resources, and allows for missing-data imputation for various species in different contexts.

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