TACI: An ImageJ Plugin for 3D Calcium Imaging Analysis

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dc.contributor.authorOmelchenko, Alisa A.en
dc.contributor.authorBai, Huaen
dc.contributor.authorHussain, Sibtainen
dc.contributor.authorTyrrell, Jordan J.en
dc.contributor.authorKlein, Masonen
dc.contributor.authorNi, Linaen
dc.date.accessioned2024-02-12T14:29:52Zen
dc.date.available2024-02-12T14:29:52Zen
dc.date.issued2022-12-16en
dc.description.abstractResearch in neuroscience has evolved to use complex imaging and computational tools to extract comprehensive information from data sets. Calcium imaging is a widely used technique that requires sophisticated software to obtain reliable results, but many laboratories struggle to adopt computational methods when updating protocols to meet modern standards. Difficulties arise due to a lack of programming knowledge and paywalls for software. In addition, cells of interest display movements in all directions during calcium imaging. Many approaches have been developed to correct the motion in the lateral (x/y) direction. This paper describes a workflow using a new ImageJ plugin, TrackMate Analysis of Calcium Imaging (TACI), to examine motion on the z-axis in 3D calcium imaging. This software identifies the maximum fluorescence value from all the z-positions a neuron appears in and uses it to represent the neuron's intensity at the corresponding t-position. Therefore, this tool can separate neurons overlapping in the lateral (x/ y) direction but appearing on distinct z-planes. As an ImageJ plugin, TACI is a user-friendly, open-source computational tool for 3D calcium imaging analysis. We validated this workflow using fly larval thermosensitive neurons that displayed movements in all directions during temperature fluctuation and a 3D calcium imaging dataset acquired from the fly brain.en
dc.description.versionAccepted versionen
dc.format.extent15 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3791/64953en
dc.identifier.eissn1940-087Xen
dc.identifier.issn1940-087Xen
dc.identifier.issue190en
dc.identifier.orcidNi, Lina [0000-0003-2155-5155]en
dc.identifier.pmid36591984en
dc.identifier.urihttps://hdl.handle.net/10919/117919en
dc.identifier.volume2022en
dc.language.isoenen
dc.publisherJournal of Visualized Experimentsen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/36591984en
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subject.meshBrainen
dc.subject.meshNeuronsen
dc.subject.meshCalciumen
dc.subject.meshImaging, Three-Dimensionalen
dc.subject.meshImage Processing, Computer-Assisteden
dc.subject.meshSoftwareen
dc.titleTACI: An ImageJ Plugin for 3D Calcium Imaging Analysisen
dc.title.serialJove-Journal of Visualized Experimentsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen
pubs.organisational-group/Virginia Tech/Science/School of Neuroscienceen

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