IOCBIO Sparks detection and analysis software
Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic c...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2019-03-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/6652.pdf |
| _version_ | 1797419805847846912 |
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| author | Martin Laasmaa Niina Karro Rikke Birkedal Marko Vendelin |
| author_facet | Martin Laasmaa Niina Karro Rikke Birkedal Marko Vendelin |
| author_sort | Martin Laasmaa |
| collection | DOAJ |
| description | Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development. |
| first_indexed | 2024-03-09T06:53:36Z |
| format | Article |
| id | doaj.art-da966f64235d4131b2ddb1c388f13def |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:53:36Z |
| publishDate | 2019-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-da966f64235d4131b2ddb1c388f13def2023-12-03T10:16:16ZengPeerJ Inc.PeerJ2167-83592019-03-017e665210.7717/peerj.6652IOCBIO Sparks detection and analysis softwareMartin LaasmaaNiina KarroRikke BirkedalMarko VendelinAnalysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.https://peerj.com/articles/6652.pdfAnalysis softwareOpen sourceCardiomyocyteCalcium sparkMouseConfocal microscopy |
| spellingShingle | Martin Laasmaa Niina Karro Rikke Birkedal Marko Vendelin IOCBIO Sparks detection and analysis software PeerJ Analysis software Open source Cardiomyocyte Calcium spark Mouse Confocal microscopy |
| title | IOCBIO Sparks detection and analysis software |
| title_full | IOCBIO Sparks detection and analysis software |
| title_fullStr | IOCBIO Sparks detection and analysis software |
| title_full_unstemmed | IOCBIO Sparks detection and analysis software |
| title_short | IOCBIO Sparks detection and analysis software |
| title_sort | iocbio sparks detection and analysis software |
| topic | Analysis software Open source Cardiomyocyte Calcium spark Mouse Confocal microscopy |
| url | https://peerj.com/articles/6652.pdf |
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