An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy
Single-photon-based head-mounted microscopy is widely used to record the brain activities of freely-moving animals. However, during data acquisition, the free movement of animals will cause shaking in the field of view, which deteriorates subsequent neural signal analyses. Existing motion correction...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Neural Circuits |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fncir.2022.891825/full |
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| author | Mingkang Li Mingkang Li Changhao Liu Changhao Liu Xin Cui Hayoung Jung Heecheon You Linqing Feng Shaomin Zhang Shaomin Zhang |
| author_facet | Mingkang Li Mingkang Li Changhao Liu Changhao Liu Xin Cui Hayoung Jung Heecheon You Linqing Feng Shaomin Zhang Shaomin Zhang |
| author_sort | Mingkang Li |
| collection | DOAJ |
| description | Single-photon-based head-mounted microscopy is widely used to record the brain activities of freely-moving animals. However, during data acquisition, the free movement of animals will cause shaking in the field of view, which deteriorates subsequent neural signal analyses. Existing motion correction methods applied to calcium imaging data either focus on offline analyses or lack sufficient accuracy in real-time processing for single-photon data. In this study, we proposed an open-source real-time motion correction (RTMC) plug-in for single-photon calcium imaging data acquisition. The RTMC plug-in is a real-time subpixel registration algorithm that can run GPUs in UCLA Miniscope data acquisition software. When used with the UCLA Miniscope, the RTMC algorithm satisfies real-time processing requirements in terms of speed, memory, and accuracy. We tested the RTMC algorithm by extending a manual neuron labeling function to extract calcium signals in a real experimental setting. The results demonstrated that the neural calcium dynamics and calcium events can be restored with high accuracy from the calcium data that were collected by the UCLA Miniscope system embedded with our RTMC plug-in. Our method could become an essential component in brain science research, where real-time brain activity is needed for closed-loop experiments. |
| first_indexed | 2024-04-13T19:49:16Z |
| format | Article |
| id | doaj.art-7830fc0d87404ebcbef1afd284ebe68e |
| institution | Directory Open Access Journal |
| issn | 1662-5110 |
| language | English |
| last_indexed | 2024-04-13T19:49:16Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neural Circuits |
| spelling | doaj.art-7830fc0d87404ebcbef1afd284ebe68e2022-12-22T02:32:36ZengFrontiers Media S.A.Frontiers in Neural Circuits1662-51102022-06-011610.3389/fncir.2022.891825891825An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted MicroscopyMingkang Li0Mingkang Li1Changhao Liu2Changhao Liu3Xin Cui4Hayoung Jung5Heecheon You6Linqing Feng7Shaomin Zhang8Shaomin Zhang9Key Laboratory of Biomedical Engineering of Education Ministry, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, School of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, ChinaQiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, ChinaKey Laboratory of Biomedical Engineering of Education Ministry, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, School of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, ChinaQiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, ChinaDepartment of Industrial and Management Engineering, Pohang University of Science and Technology, Pohang, South KoreaDepartment of Industrial and Management Engineering, Pohang University of Science and Technology, Pohang, South KoreaDepartment of Industrial and Management Engineering, Pohang University of Science and Technology, Pohang, South KoreaResearch Institute of Artificial Intelligence, Zhejiang Lab, Hangzhou, ChinaKey Laboratory of Biomedical Engineering of Education Ministry, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, School of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, ChinaQiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, ChinaSingle-photon-based head-mounted microscopy is widely used to record the brain activities of freely-moving animals. However, during data acquisition, the free movement of animals will cause shaking in the field of view, which deteriorates subsequent neural signal analyses. Existing motion correction methods applied to calcium imaging data either focus on offline analyses or lack sufficient accuracy in real-time processing for single-photon data. In this study, we proposed an open-source real-time motion correction (RTMC) plug-in for single-photon calcium imaging data acquisition. The RTMC plug-in is a real-time subpixel registration algorithm that can run GPUs in UCLA Miniscope data acquisition software. When used with the UCLA Miniscope, the RTMC algorithm satisfies real-time processing requirements in terms of speed, memory, and accuracy. We tested the RTMC algorithm by extending a manual neuron labeling function to extract calcium signals in a real experimental setting. The results demonstrated that the neural calcium dynamics and calcium events can be restored with high accuracy from the calcium data that were collected by the UCLA Miniscope system embedded with our RTMC plug-in. Our method could become an essential component in brain science research, where real-time brain activity is needed for closed-loop experiments.https://www.frontiersin.org/articles/10.3389/fncir.2022.891825/fullcalcium imagingmotion correctionsingle-photon microscopyreal-timeopen-source |
| spellingShingle | Mingkang Li Mingkang Li Changhao Liu Changhao Liu Xin Cui Hayoung Jung Heecheon You Linqing Feng Shaomin Zhang Shaomin Zhang An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy Frontiers in Neural Circuits calcium imaging motion correction single-photon microscopy real-time open-source |
| title | An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy |
| title_full | An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy |
| title_fullStr | An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy |
| title_full_unstemmed | An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy |
| title_short | An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy |
| title_sort | open source real time motion correction plug in for single photon calcium imaging of head mounted microscopy |
| topic | calcium imaging motion correction single-photon microscopy real-time open-source |
| url | https://www.frontiersin.org/articles/10.3389/fncir.2022.891825/full |
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