Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding
Abstract As a key pathway for understanding behavior, cognition, and emotion, neural decoding and encoding provide effective tools to bridge the gap between neural mechanisms and imaging recordings, especially at single-cell resolution. While neural decoding aims to establish an interpretable theory...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-05-01
|
| Series: | Journal of NeuroEngineering and Rehabilitation |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12984-025-01655-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849704247089692672 |
|---|---|
| author | Kangchen Li Huanwei Liang Jialing Qiu Xulan Zhang Bobo Cai Depeng Wang Diming Zhang Bingzhi Lin Haijun Han Geng Yang Zhijing Zhu |
| author_facet | Kangchen Li Huanwei Liang Jialing Qiu Xulan Zhang Bobo Cai Depeng Wang Diming Zhang Bingzhi Lin Haijun Han Geng Yang Zhijing Zhu |
| author_sort | Kangchen Li |
| collection | DOAJ |
| description | Abstract As a key pathway for understanding behavior, cognition, and emotion, neural decoding and encoding provide effective tools to bridge the gap between neural mechanisms and imaging recordings, especially at single-cell resolution. While neural decoding aims to establish an interpretable theory of how complex biological behaviors are represented in neural activities, neural encoding focuses on manipulating behaviors through the stimulation of specific neurons. We thoroughly analyze the application of fluorescence imaging techniques, particularly two-photon fluorescence imaging, in decoding neural activities, showcasing the theoretical analysis and technological advancements from imaging recording to behavioral manipulation. For decoding models, we compared linear and nonlinear methods, including independent component analysis, random forests, and support vector machines, highlighting their capabilities to reveal the intricate mapping between neural activity and behavior. By employing synthetic stimuli via optogenetics, fundamental principles of neural encoding are further explored. We elucidate various encoding types based on different stimulus paradigms—quantity encoding, spatial encoding, temporal encoding, and frequency encoding—enhancing our understanding of how the brain represents and processes information. We believe that fluorescence imaging-based neural decoding and encoding techniques have deepened our understanding of the brain, and hold great potential in paving the way for future neuroscience research and clinical applications. |
| format | Article |
| id | doaj-art-d4d4b9daf87f400a861975fd436e30a3 |
| institution | DOAJ |
| issn | 1743-0003 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of NeuroEngineering and Rehabilitation |
| spelling | doaj-art-d4d4b9daf87f400a861975fd436e30a32025-08-20T03:16:50ZengBMCJournal of NeuroEngineering and Rehabilitation1743-00032025-05-0122111510.1186/s12984-025-01655-3Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encodingKangchen Li0Huanwei Liang1Jialing Qiu2Xulan Zhang3Bobo Cai4Depeng Wang5Diming Zhang6Bingzhi Lin7Haijun Han8Geng Yang9Zhijing Zhu10Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityZhejiang HospitalCollege of Energy and Power Engineering, Nanjing University of Aeronautics and AstronauticsResearch Center for Intelligent Sensing Systems, Zhejiang LaboratoryCollege of Energy and Power Engineering, Nanjing University of Aeronautics and AstronauticsKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Institute of Brain and Cognitive Science, School of Medicine, Hangzhou City UniversityAbstract As a key pathway for understanding behavior, cognition, and emotion, neural decoding and encoding provide effective tools to bridge the gap between neural mechanisms and imaging recordings, especially at single-cell resolution. While neural decoding aims to establish an interpretable theory of how complex biological behaviors are represented in neural activities, neural encoding focuses on manipulating behaviors through the stimulation of specific neurons. We thoroughly analyze the application of fluorescence imaging techniques, particularly two-photon fluorescence imaging, in decoding neural activities, showcasing the theoretical analysis and technological advancements from imaging recording to behavioral manipulation. For decoding models, we compared linear and nonlinear methods, including independent component analysis, random forests, and support vector machines, highlighting their capabilities to reveal the intricate mapping between neural activity and behavior. By employing synthetic stimuli via optogenetics, fundamental principles of neural encoding are further explored. We elucidate various encoding types based on different stimulus paradigms—quantity encoding, spatial encoding, temporal encoding, and frequency encoding—enhancing our understanding of how the brain represents and processes information. We believe that fluorescence imaging-based neural decoding and encoding techniques have deepened our understanding of the brain, and hold great potential in paving the way for future neuroscience research and clinical applications.https://doi.org/10.1186/s12984-025-01655-3Neural imagingMathematical modelOptogeneticsNeural decodingNeural encoding |
| spellingShingle | Kangchen Li Huanwei Liang Jialing Qiu Xulan Zhang Bobo Cai Depeng Wang Diming Zhang Bingzhi Lin Haijun Han Geng Yang Zhijing Zhu Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding Journal of NeuroEngineering and Rehabilitation Neural imaging Mathematical model Optogenetics Neural decoding Neural encoding |
| title | Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding |
| title_full | Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding |
| title_fullStr | Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding |
| title_full_unstemmed | Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding |
| title_short | Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding |
| title_sort | reveal the mechanism of brain function with fluorescence microscopy at single cell resolution from neural decoding to encoding |
| topic | Neural imaging Mathematical model Optogenetics Neural decoding Neural encoding |
| url | https://doi.org/10.1186/s12984-025-01655-3 |
| work_keys_str_mv | AT kangchenli revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT huanweiliang revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT jialingqiu revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT xulanzhang revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT bobocai revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT depengwang revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT dimingzhang revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT bingzhilin revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT haijunhan revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT gengyang revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding AT zhijingzhu revealthemechanismofbrainfunctionwithfluorescencemicroscopyatsinglecellresolutionfromneuraldecodingtoencoding |