Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields
Significance: Light-field microscopy (LFM) enables fast, light-efficient, volumetric imaging of neuronal activity with calcium indicators. Calcium transients differ in temporal signal-to-noise ratio (tSNR) and spatial confinement when extracted from volumes reconstructed by different algorithms. Aim...
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| Veröffentlicht in: | Neurophotonics (Print) 2022-10, Vol.9 (4), p.041404-041404 |
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| creator | Howe, Carmel L. Quicke, Peter Song, Pingfan Verinaz-Jadan, Herman Dragotti, Pier Luigi Foust, Amanda J. |
| description | Significance: Light-field microscopy (LFM) enables fast, light-efficient, volumetric imaging of neuronal activity with calcium indicators. Calcium transients differ in temporal signal-to-noise ratio (tSNR) and spatial confinement when extracted from volumes reconstructed by different algorithms.
Aim: We evaluated the capabilities and limitations of two light-field reconstruction algorithms for calcium fluorescence imaging.
Approach: We acquired light-field image series from neurons either bulk-labeled or filled intracellularly with the red-emitting calcium dye CaSiR-1 in acute mouse brain slices. We compared the tSNR and spatial confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson–Lucy three-dimensional deconvolution with and without total variation regularization.
Results: Both synthetic refocusing and Richardson–Lucy deconvolution resolved calcium signals from single cells and neuronal dendrites in three dimensions. Increasing deconvolution iteration number improved spatial confinement but reduced tSNR compared with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes.
Conclusions: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly loaded). The trade-offs identified for tSNR, spatial confinement, and computational cost indicate which of synthetic refocusing or deconvolution can better realize the scientific requirements of future LFM calcium imaging applications. |
| doi_str_mv | 10.1117/1.NPh.9.4.041404 |
| format | Article |
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Aim: We evaluated the capabilities and limitations of two light-field reconstruction algorithms for calcium fluorescence imaging.
Approach: We acquired light-field image series from neurons either bulk-labeled or filled intracellularly with the red-emitting calcium dye CaSiR-1 in acute mouse brain slices. We compared the tSNR and spatial confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson–Lucy three-dimensional deconvolution with and without total variation regularization.
Results: Both synthetic refocusing and Richardson–Lucy deconvolution resolved calcium signals from single cells and neuronal dendrites in three dimensions. Increasing deconvolution iteration number improved spatial confinement but reduced tSNR compared with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes.
Conclusions: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly loaded). The trade-offs identified for tSNR, spatial confinement, and computational cost indicate which of synthetic refocusing or deconvolution can better realize the scientific requirements of future LFM calcium imaging applications.</description><identifier>ISSN: 2329-423X</identifier><identifier>EISSN: 2329-4248</identifier><identifier>DOI: 10.1117/1.NPh.9.4.041404</identifier><identifier>PMID: 35445141</identifier><language>eng</language><publisher>United States: Society of Photo-Optical Instrumentation Engineers</publisher><subject>Algorithms ; Brain slice preparation ; Calcium imaging ; Calcium signalling ; Cameras ; Computational neuroscience ; Dendrites ; Ions ; Light emitting diodes ; Localization ; Neuroimaging ; Neurons ; Potassium ; Special Section on Computational Approaches for Neuroimaging ; Three dimensional imaging</subject><ispartof>Neurophotonics (Print), 2022-10, Vol.9 (4), p.041404-041404</ispartof><rights>The Authors. Published by SPIE under a Creative Commons Attribution 4.0 International License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.</rights><rights>2022 The Authors.</rights><rights>2022. This work is licensed under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 The Authors 2022 The Authors</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c462t-9f7877664eaff0ce6848a75a3072d04b5dd75f63967de8ac9e980163daaddf503</citedby><orcidid>0000-0003-1391-3426 ; 0000-0002-5827-8705 ; 0000-0002-4895-0502 ; 0000-0002-6073-2807 ; 0000-0003-2289-6672</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2858381602/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2858381602?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,21387,27923,27924,33743,33744,43804,53790,53792,64384,64386,64388,72340,74173</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35445141$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Howe, Carmel L.</creatorcontrib><creatorcontrib>Quicke, Peter</creatorcontrib><creatorcontrib>Song, Pingfan</creatorcontrib><creatorcontrib>Verinaz-Jadan, Herman</creatorcontrib><creatorcontrib>Dragotti, Pier Luigi</creatorcontrib><creatorcontrib>Foust, Amanda J.</creatorcontrib><title>Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields</title><title>Neurophotonics (Print)</title><addtitle>Neurophoton</addtitle><description>Significance: Light-field microscopy (LFM) enables fast, light-efficient, volumetric imaging of neuronal activity with calcium indicators. Calcium transients differ in temporal signal-to-noise ratio (tSNR) and spatial confinement when extracted from volumes reconstructed by different algorithms.
Aim: We evaluated the capabilities and limitations of two light-field reconstruction algorithms for calcium fluorescence imaging.
Approach: We acquired light-field image series from neurons either bulk-labeled or filled intracellularly with the red-emitting calcium dye CaSiR-1 in acute mouse brain slices. We compared the tSNR and spatial confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson–Lucy three-dimensional deconvolution with and without total variation regularization.
Results: Both synthetic refocusing and Richardson–Lucy deconvolution resolved calcium signals from single cells and neuronal dendrites in three dimensions. Increasing deconvolution iteration number improved spatial confinement but reduced tSNR compared with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes.
Conclusions: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly loaded). The trade-offs identified for tSNR, spatial confinement, and computational cost indicate which of synthetic refocusing or deconvolution can better realize the scientific requirements of future LFM calcium imaging applications.</description><subject>Algorithms</subject><subject>Brain slice preparation</subject><subject>Calcium imaging</subject><subject>Calcium signalling</subject><subject>Cameras</subject><subject>Computational neuroscience</subject><subject>Dendrites</subject><subject>Ions</subject><subject>Light emitting diodes</subject><subject>Localization</subject><subject>Neuroimaging</subject><subject>Neurons</subject><subject>Potassium</subject><subject>Special Section on Computational Approaches for Neuroimaging</subject><subject>Three dimensional imaging</subject><issn>2329-423X</issn><issn>2329-4248</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1kcuLFDEQxoMo7rLu3ZMEvHjpNu9OLoIMvmBRDwreQjaPmSzdyZikF_e_N7uzjg_wVEXVr75U6gPgKUYjxnh6icePn3ejGtmIGGaIPQCnhBI1MMLkw2NOv52A81qvEEKYYMUxfQxOKGeMY4ZPQd3kZW9KTFtYb1Lb-RYtLD5ku9bbYsvQeZvTdZ7XFnOCIRfYMeh_tGLsXSkHmPxacjIztGa2cV1gb6YafWoVhpIXOMftrsEQ_ezqE_AomLn68_t4Br6-ffNl8364-PTuw-b1xWCZIG1QYZLTJATzJgRkvZBMmokbiibiELvkzk08CKrE5Lw0VnklERbUGeNc4IiegVcH3f16uXhn-zbFzHpf4mLKjc4m6r87Ke70Nl9rqQhBdwIv7gVK_r762vQSq_XzbJLPa9VEcEqE4Ip19Pk_6FVeS79IpySXVGKBSKfQgbIl19rPfFwGI31rqsa6m6qVZvpgah959ucnjgO_LOzAcADqPvrfr_5X8Cej867T</recordid><startdate>20221001</startdate><enddate>20221001</enddate><creator>Howe, Carmel L.</creator><creator>Quicke, Peter</creator><creator>Song, Pingfan</creator><creator>Verinaz-Jadan, Herman</creator><creator>Dragotti, Pier Luigi</creator><creator>Foust, Amanda J.</creator><general>Society of Photo-Optical Instrumentation Engineers</general><general>S P I E - International Society for</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-1391-3426</orcidid><orcidid>https://orcid.org/0000-0002-5827-8705</orcidid><orcidid>https://orcid.org/0000-0002-4895-0502</orcidid><orcidid>https://orcid.org/0000-0002-6073-2807</orcidid><orcidid>https://orcid.org/0000-0003-2289-6672</orcidid></search><sort><creationdate>20221001</creationdate><title>Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields</title><author>Howe, Carmel L. ; Quicke, Peter ; Song, Pingfan ; Verinaz-Jadan, Herman ; Dragotti, Pier Luigi ; Foust, Amanda J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c462t-9f7877664eaff0ce6848a75a3072d04b5dd75f63967de8ac9e980163daaddf503</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Algorithms</topic><topic>Brain slice preparation</topic><topic>Calcium imaging</topic><topic>Calcium signalling</topic><topic>Cameras</topic><topic>Computational neuroscience</topic><topic>Dendrites</topic><topic>Ions</topic><topic>Light emitting diodes</topic><topic>Localization</topic><topic>Neuroimaging</topic><topic>Neurons</topic><topic>Potassium</topic><topic>Special Section on Computational Approaches for Neuroimaging</topic><topic>Three dimensional imaging</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Howe, Carmel L.</creatorcontrib><creatorcontrib>Quicke, Peter</creatorcontrib><creatorcontrib>Song, Pingfan</creatorcontrib><creatorcontrib>Verinaz-Jadan, Herman</creatorcontrib><creatorcontrib>Dragotti, Pier Luigi</creatorcontrib><creatorcontrib>Foust, Amanda J.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Neurophotonics (Print)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Howe, Carmel L.</au><au>Quicke, Peter</au><au>Song, Pingfan</au><au>Verinaz-Jadan, Herman</au><au>Dragotti, Pier Luigi</au><au>Foust, Amanda J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields</atitle><jtitle>Neurophotonics (Print)</jtitle><addtitle>Neurophoton</addtitle><date>2022-10-01</date><risdate>2022</risdate><volume>9</volume><issue>4</issue><spage>041404</spage><epage>041404</epage><pages>041404-041404</pages><issn>2329-423X</issn><eissn>2329-4248</eissn><abstract>Significance: Light-field microscopy (LFM) enables fast, light-efficient, volumetric imaging of neuronal activity with calcium indicators. Calcium transients differ in temporal signal-to-noise ratio (tSNR) and spatial confinement when extracted from volumes reconstructed by different algorithms.
Aim: We evaluated the capabilities and limitations of two light-field reconstruction algorithms for calcium fluorescence imaging.
Approach: We acquired light-field image series from neurons either bulk-labeled or filled intracellularly with the red-emitting calcium dye CaSiR-1 in acute mouse brain slices. We compared the tSNR and spatial confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson–Lucy three-dimensional deconvolution with and without total variation regularization.
Results: Both synthetic refocusing and Richardson–Lucy deconvolution resolved calcium signals from single cells and neuronal dendrites in three dimensions. Increasing deconvolution iteration number improved spatial confinement but reduced tSNR compared with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes.
Conclusions: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly loaded). The trade-offs identified for tSNR, spatial confinement, and computational cost indicate which of synthetic refocusing or deconvolution can better realize the scientific requirements of future LFM calcium imaging applications.</abstract><cop>United States</cop><pub>Society of Photo-Optical Instrumentation Engineers</pub><pmid>35445141</pmid><doi>10.1117/1.NPh.9.4.041404</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-1391-3426</orcidid><orcidid>https://orcid.org/0000-0002-5827-8705</orcidid><orcidid>https://orcid.org/0000-0002-4895-0502</orcidid><orcidid>https://orcid.org/0000-0002-6073-2807</orcidid><orcidid>https://orcid.org/0000-0003-2289-6672</orcidid><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; ProQuest Central UK/Ireland; PubMed Central; ProQuest Central |
| subjects | Algorithms Brain slice preparation Calcium imaging Calcium signalling Cameras Computational neuroscience Dendrites Ions Light emitting diodes Localization Neuroimaging Neurons Potassium Special Section on Computational Approaches for Neuroimaging Three dimensional imaging |
| title | Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields |
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