moco: Fast Motion Correction for Calcium Imaging
Motion correction is the first step in a pipeline of algorithms to analyze calcium imaging videos and extract biologically relevant information, for example the network structure of the neurons therein. Fast motion correction is especially critical for closed-loop activity triggered stimulation expe...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2016-02-01
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| Series: | Frontiers in Neuroinformatics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fninf.2016.00006/full |
| _version_ | 1818890989989789696 |
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| author | Alexander eDubbs Rafael eYuste James eGuevara |
| author_facet | Alexander eDubbs Rafael eYuste James eGuevara |
| author_sort | Alexander eDubbs |
| collection | DOAJ |
| description | Motion correction is the first step in a pipeline of algorithms to analyze calcium imaging videos and extract biologically relevant information, for example the network structure of the neurons therein. Fast motion correction is especially critical for closed-loop activity triggered stimulation experiments, where accurate detection and targeting of specific cells in necessary. We introduce a novel motion-correction algorithm that uses a Fourier-transform approach, and a combination of judicious downsampling and the accelerated computation of many $L_2$ norms using dynamic programming and two-dimensional, fft-accelerated convolutions, to enhance its efficiency. Its accuracy is comparable to that of established community-used algorithms, and it is more stable to large translational motions. It is programmed in Java and is compatible with ImageJ. |
| first_indexed | 2024-12-19T17:33:41Z |
| format | Article |
| id | doaj.art-9d854a54895e46d093058d4993d9fc64 |
| institution | Directory Open Access Journal |
| issn | 1662-5196 |
| language | English |
| last_indexed | 2024-12-19T17:33:41Z |
| publishDate | 2016-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj.art-9d854a54895e46d093058d4993d9fc642022-12-21T20:12:24ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962016-02-011010.3389/fninf.2016.00006173364moco: Fast Motion Correction for Calcium ImagingAlexander eDubbs0Rafael eYuste1James eGuevara2Columbia UniversityColumbia UniversityColumbia UniversityMotion correction is the first step in a pipeline of algorithms to analyze calcium imaging videos and extract biologically relevant information, for example the network structure of the neurons therein. Fast motion correction is especially critical for closed-loop activity triggered stimulation experiments, where accurate detection and targeting of specific cells in necessary. We introduce a novel motion-correction algorithm that uses a Fourier-transform approach, and a combination of judicious downsampling and the accelerated computation of many $L_2$ norms using dynamic programming and two-dimensional, fft-accelerated convolutions, to enhance its efficiency. Its accuracy is comparable to that of established community-used algorithms, and it is more stable to large translational motions. It is programmed in Java and is compatible with ImageJ.http://journal.frontiersin.org/Journal/10.3389/fninf.2016.00006/fullDynamic Programmingcalcium imagingMotion CorrectionFourier TransformMesoscale Neuroscience |
| spellingShingle | Alexander eDubbs Rafael eYuste James eGuevara moco: Fast Motion Correction for Calcium Imaging Frontiers in Neuroinformatics Dynamic Programming calcium imaging Motion Correction Fourier Transform Mesoscale Neuroscience |
| title | moco: Fast Motion Correction for Calcium Imaging |
| title_full | moco: Fast Motion Correction for Calcium Imaging |
| title_fullStr | moco: Fast Motion Correction for Calcium Imaging |
| title_full_unstemmed | moco: Fast Motion Correction for Calcium Imaging |
| title_short | moco: Fast Motion Correction for Calcium Imaging |
| title_sort | moco fast motion correction for calcium imaging |
| topic | Dynamic Programming calcium imaging Motion Correction Fourier Transform Mesoscale Neuroscience |
| url | http://journal.frontiersin.org/Journal/10.3389/fninf.2016.00006/full |
| work_keys_str_mv | AT alexanderedubbs mocofastmotioncorrectionforcalciumimaging AT rafaeleyuste mocofastmotioncorrectionforcalciumimaging AT jameseguevara mocofastmotioncorrectionforcalciumimaging |