CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data
Abstract Background Calcium imaging is a powerful technique for recording cellular activity across large populations of neurons. However, analysis methods capable of single-cell resolution in cultured neurons, especially for cultures derived from human induced pluripotent stem cells (hiPSCs), are la...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-11-01
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| Series: | BMC Neuroscience |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12868-022-00751-7 |
| _version_ | 1811207766580133888 |
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| author | Madhavi Tippani Elizabeth A. Pattie Brittany A. Davis Claudia V. Nguyen Yanhong Wang Srinidhi Rao Sripathy Brady J. Maher Keri Martinowich Andrew E. Jaffe Stephanie Cerceo Page |
| author_facet | Madhavi Tippani Elizabeth A. Pattie Brittany A. Davis Claudia V. Nguyen Yanhong Wang Srinidhi Rao Sripathy Brady J. Maher Keri Martinowich Andrew E. Jaffe Stephanie Cerceo Page |
| author_sort | Madhavi Tippani |
| collection | DOAJ |
| description | Abstract Background Calcium imaging is a powerful technique for recording cellular activity across large populations of neurons. However, analysis methods capable of single-cell resolution in cultured neurons, especially for cultures derived from human induced pluripotent stem cells (hiPSCs), are lacking. Existing methods lack scalability to accommodate high-throughput comparisons between multiple lines, across developmental timepoints, or across pharmacological manipulations. Results To address this need we developed CaPTure, a scalable, automated Ca2+ imaging analysis pipeline ( https://github.com/LieberInstitute/CaPTure ). CaPTuredetects neurons, classifies and quantifies spontaneous activity, quantifies synchrony metrics, and generates cell- and network-specific metrics that facilitate phenotypic discovery. The method is compatible with parallel processing on computing clusters without requiring significant user input or parameter modification. Conclusion CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems. |
| first_indexed | 2024-04-12T04:10:21Z |
| format | Article |
| id | doaj.art-eb56475a8b4b4772b6ccf8c3a8d880ff |
| institution | Directory Open Access Journal |
| issn | 1471-2202 |
| language | English |
| last_indexed | 2024-04-12T04:10:21Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Neuroscience |
| spelling | doaj.art-eb56475a8b4b4772b6ccf8c3a8d880ff2022-12-22T03:48:31ZengBMCBMC Neuroscience1471-22022022-11-0123111410.1186/s12868-022-00751-7CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging dataMadhavi Tippani0Elizabeth A. Pattie1Brittany A. Davis2Claudia V. Nguyen3Yanhong Wang4Srinidhi Rao Sripathy5Brady J. Maher6Keri Martinowich7Andrew E. Jaffe8Stephanie Cerceo Page9Lieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusAbstract Background Calcium imaging is a powerful technique for recording cellular activity across large populations of neurons. However, analysis methods capable of single-cell resolution in cultured neurons, especially for cultures derived from human induced pluripotent stem cells (hiPSCs), are lacking. Existing methods lack scalability to accommodate high-throughput comparisons between multiple lines, across developmental timepoints, or across pharmacological manipulations. Results To address this need we developed CaPTure, a scalable, automated Ca2+ imaging analysis pipeline ( https://github.com/LieberInstitute/CaPTure ). CaPTuredetects neurons, classifies and quantifies spontaneous activity, quantifies synchrony metrics, and generates cell- and network-specific metrics that facilitate phenotypic discovery. The method is compatible with parallel processing on computing clusters without requiring significant user input or parameter modification. Conclusion CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems.https://doi.org/10.1186/s12868-022-00751-7Calcium imaginghiPSCNeuronal activityImage analysis |
| spellingShingle | Madhavi Tippani Elizabeth A. Pattie Brittany A. Davis Claudia V. Nguyen Yanhong Wang Srinidhi Rao Sripathy Brady J. Maher Keri Martinowich Andrew E. Jaffe Stephanie Cerceo Page CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data BMC Neuroscience Calcium imaging hiPSC Neuronal activity Image analysis |
| title | CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data |
| title_full | CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data |
| title_fullStr | CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data |
| title_full_unstemmed | CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data |
| title_short | CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data |
| title_sort | capture calcium peaktoolbox for analysis of in vitro calcium imaging data |
| topic | Calcium imaging hiPSC Neuronal activity Image analysis |
| url | https://doi.org/10.1186/s12868-022-00751-7 |
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