{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T05:55:23Z","timestamp":1782885323564,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011060","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T00:00:00Z","timestamp":1684108800000}}],"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2023,4,21]],"date-time":"2023-04-21T00:00:00Z","timestamp":1682035200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006792","name":"Hartwell Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006792","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1DP2GM150022-01"],"award-info":[{"award-number":["1DP2GM150022-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Mitochondria form a network in the cell that rapidly changes through fission, fusion, and motility. Dysregulation of this four-dimensional (4D: x,y,z,time) network is implicated in numerous diseases ranging from cancer to neurodegeneration. While lattice light-sheet microscopy has recently made it possible to image mitochondria in 4D, quantitative analysis methods for the resulting datasets have been lacking. Here we present MitoTNT, the first-in-class software for<jats:underline>Mito<\/jats:underline>chondrial<jats:underline>T<\/jats:underline>emporal<jats:underline>N<\/jats:underline>etwork<jats:underline>T<\/jats:underline>racking in 4D live-cell fluorescence microscopy data. MitoTNT uses spatial proximity and network topology to compute an optimal tracking assignment. To validate the accuracy of tracking, we created a reaction-diffusion simulation to model mitochondrial network motion and remodeling events. We found that our tracking is &gt;90% accurate for ground-truth simulations and agrees well with published motility results for experimental data. We used MitoTNT to quantify 4D mitochondrial networks from human induced pluripotent stem cells. First, we characterized sub-fragment motility and analyzed network branch motion patterns. We revealed that the skeleton node motion is correlated along branch nodes and is uncorrelated in time. Second, we identified fission and fusion events with high spatiotemporal resolution. We found that mitochondrial skeleton nodes near the fission\/fusion sites move nearly twice as fast as random skeleton nodes and that microtubules play a role in mediating selective fission\/fusion. Finally, we developed graph-based transport simulations that model how material would distribute on experimentally measured mitochondrial temporal networks. We showed that pharmacological perturbations increase network reachability but decrease network resilience through a combination of altered mitochondrial fission\/fusion dynamics and motility. MitoTNT\u2019s easy-to-use tracking module, interactive 4D visualization capability, and powerful post-tracking analyses aim at making temporal network tracking accessible to the wider mitochondria research community.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011060","type":"journal-article","created":{"date-parts":[[2023,4,21]],"date-time":"2023-04-21T17:58:47Z","timestamp":1682099927000},"page":"e1011060","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":22,"title":["MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4759-3053","authenticated-orcid":true,"given":"Zichen","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4299-0885","authenticated-orcid":true,"given":"Parth","family":"Natekar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Challana","family":"Tea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon","family":"Tamir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2503-0480","authenticated-orcid":true,"given":"Hiroyuki","family":"Hakozaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7083-1828","authenticated-orcid":true,"given":"Johannes","family":"Sch\u00f6neberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,4,21]]},"reference":[{"issue":"7318","key":"pcbi.1011060.ref001","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/nature09486","article-title":"The energetics of genome complexity","volume":"467","author":"N Lane","year":"2010","journal-title":"Nature"},{"issue":"7483","key":"pcbi.1011060.ref002","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nature12985","article-title":"Mitochondrial form and function","volume":"505","author":"JR Friedman","year":"2014","journal-title":"Nature"},{"key":"pcbi.1011060.ref003","doi-asserted-by":"crossref","first-page":"570","DOI":"10.3389\/fendo.2019.00570","article-title":"Dysregulated Mitochondrial Dynamics and Metabolism in Obesity, Diabetes, and Cancer","volume":"10","author":"W Dai","year":"2019","journal-title":"Front Endocrinol"},{"key":"pcbi.1011060.ref004","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.neubiorev.2014.01.012","article-title":"Mitochondrial dysfunction as a central actor in intellectual disability-related diseases: An overview of Down syndrome, autism, Fragile X and Rett syndrome","volume":"46","author":"D Valenti","year":"2014","journal-title":"Neurosci Biobehav Rev"},{"issue":"1","key":"pcbi.1011060.ref005","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.mito.2011.04.004","article-title":"Mitochondrial dysfunction in epilepsy","volume":"12","author":"J Folbergrov\u00e1","year":"2012","journal-title":"Mitochondrion"},{"issue":"2","key":"pcbi.1011060.ref006","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.tcb.2012.10.006","article-title":"Mitochondrial dynamics in neurodegeneration","volume":"23","author":"K Itoh","year":"2013","journal-title":"Trends Cell Biol"},{"key":"pcbi.1011060.ref007","doi-asserted-by":"crossref","first-page":"138","DOI":"10.3389\/fncel.2020.00138","article-title":"Abnormal Mitochondrial Quality Control in Neurodegenerative Diseases","volume":"14","author":"X Yan","year":"2020","journal-title":"Front Cell Neurosci"},{"key":"pcbi.1011060.ref008","doi-asserted-by":"crossref","first-page":"359","DOI":"10.3389\/fnins.2021.654785","article-title":"Mitochondrial Dynamics: A Key Role in Neurodegeneration and a Potential Target for Neurodegenerative Disease","volume":"15","author":"D Yang","year":"2021","journal-title":"Front Neurosci"},{"key":"pcbi.1011060.ref009","doi-asserted-by":"crossref","first-page":"413","DOI":"10.3389\/fcell.2020.00413","article-title":"The Role of Mitochondrial Dynamics and Mitophagy in Carcinogenesis, Metastasis and Therapy","volume":"8","author":"Y Wang","year":"2020","journal-title":"Front Cell Dev Biol"},{"issue":"8","key":"pcbi.1011060.ref010","doi-asserted-by":"crossref","DOI":"10.1242\/dev.143420","article-title":"The role of mitochondria in stem cell fate and aging","volume":"145","author":"H Zhang","year":"2018","journal-title":"Development"},{"key":"pcbi.1011060.ref011","doi-asserted-by":"crossref","first-page":"111212","DOI":"10.1016\/j.mad.2020.111212","article-title":"Mitochondrial fission and fusion: A dynamic role in aging and potential target for age-related disease","volume":"186","author":"YJ Liu","year":"2020","journal-title":"Mech Ageing Dev"},{"issue":"6208","key":"pcbi.1011060.ref012","doi-asserted-by":"crossref","first-page":"1257998","DOI":"10.1126\/science.1257998","article-title":"Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution","volume":"346","author":"BC Chen","year":"2014","journal-title":"Science"},{"issue":"6386","key":"pcbi.1011060.ref013","doi-asserted-by":"crossref","first-page":"eaaq1392","DOI":"10.1126\/science.aaq1392","article-title":"Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms","volume":"360","author":"TL Liu","year":"2018","journal-title":"Science"},{"issue":"7","key":"pcbi.1011060.ref014","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1093\/bioinformatics\/bts073","article-title":"Mytoe: automatic analysis of mitochondrial dynamics","volume":"28","author":"E Lihavainen","year":"2012","journal-title":"Bioinformatics"},{"issue":"7","key":"pcbi.1011060.ref015","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1002\/bit.25563","article-title":"Automated detection of whole-cell mitochondrial motility and its dependence on cytoarchitectural integrity","volume":"112","author":"J Kandel","year":"2015","journal-title":"Biotechnol Bioeng"},{"issue":"1","key":"pcbi.1011060.ref016","doi-asserted-by":"crossref","first-page":"e108","DOI":"10.1002\/cpcb.108","article-title":"QuoVadoPro, an Autonomous Tool for Measuring Intracellular Dynamics Using Temporal Variance","volume":"87","author":"H Basu","year":"2020","journal-title":"Curr Protoc Cell Biol"},{"key":"pcbi.1011060.ref017","first-page":"77","volume-title":"Methods in Cell Biology","author":"MP Viana","year":"2015"},{"key":"pcbi.1011060.ref018","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.ab.2018.02.022","article-title":"Methods for imaging mammalian mitochondrial morphology: A prospective on MitoGraph","volume":"552","author":"MC Harwig","year":"2018","journal-title":"Anal Biochem"},{"issue":"3","key":"pcbi.1011060.ref019","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.cels.2020.02.002","article-title":"Mitochondrial Fission and Fusion Dynamics Generate Efficient, Robust, and Evenly Distributed Network Topologies in Budding Yeast Cells","volume":"10","author":"MP Viana","year":"2020","journal-title":"Cell Syst"},{"key":"pcbi.1011060.ref020","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.ymeth.2016.09.016","article-title":"TrackMate: An open and extensible platform for single-particle tracking","volume":"115","author":"JY Tinevez","year":"2017","journal-title":"Methods"},{"issue":"9","key":"pcbi.1011060.ref021","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1038\/s41592-021-01234-z","article-title":"Automated segmentation and tracking of mitochondria in live-cell time-lapse images","volume":"18","author":"AEYT Lefebvre","year":"2021","journal-title":"Nat Methods"},{"issue":"1","key":"pcbi.1011060.ref022","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1002\/pro.3235","article-title":"UCSF ChimeraX: Meeting modern challenges in visualization and analysis","volume":"27","author":"TD Goddard","year":"2018","journal-title":"Protein Sci"},{"issue":"1","key":"pcbi.1011060.ref023","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: Structure visualization for researchers, educators, and developers","volume":"30","author":"EF Pettersen","year":"2021","journal-title":"Protein Sci"},{"key":"pcbi.1011060.ref024","doi-asserted-by":"crossref","unstructured":"Lowe DG. Object recognition from local scale-invariant features. In: Proceedings of the Seventh IEEE International Conference on Computer Vision. 1999. p. 1150\u20137 vol.2.","DOI":"10.1109\/ICCV.1999.790410"},{"issue":"1","key":"pcbi.1011060.ref025","doi-asserted-by":"crossref","first-page":"13924","DOI":"10.1038\/srep13924","article-title":"Structural Heterogeneity of Mitochondria Induced by the Microtubule Cytoskeleton","volume":"5","author":"VM Sukhorukov","year":"2015","journal-title":"Sci Rep"},{"issue":"8","key":"pcbi.1011060.ref026","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nmeth.1237","article-title":"Robust single-particle tracking in live-cell time-lapse sequences","volume":"5","author":"K Jaqaman","year":"2008","journal-title":"Nat Methods"},{"issue":"9","key":"pcbi.1011060.ref027","doi-asserted-by":"crossref","first-page":"e74261","DOI":"10.1371\/journal.pone.0074261","article-title":"ReaDDy\u2014A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments","volume":"8","author":"J Sch\u00f6neberg","year":"2013","journal-title":"PLOS ONE"},{"issue":"2","key":"pcbi.1011060.ref028","doi-asserted-by":"crossref","first-page":"e1006830","DOI":"10.1371\/journal.pcbi.1006830","article-title":"ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics","volume":"15","author":"M Hoffmann","year":"2019","journal-title":"PLOS Comput Biol"},{"issue":"9","key":"pcbi.1011060.ref029","doi-asserted-by":"crossref","first-page":"E947","DOI":"10.1073\/pnas.1501737112","article-title":"Integrity of the yeast mitochondrial genome, but not its distribution and inheritance, relies on mitochondrial fission and fusion","volume":"112","author":"C Osman","year":"2015","journal-title":"Proc Natl Acad Sci"},{"issue":"10","key":"pcbi.1011060.ref030","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1038\/cdd.2011.13","article-title":"Altered fusion dynamics underlie unique morphological changes in mitochondria during hypoxia\u2013reoxygenation stress","volume":"18","author":"X Liu","year":"2011","journal-title":"Cell Death Differ"},{"issue":"6054","key":"pcbi.1011060.ref031","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1126\/science.1207385","article-title":"ER Tubules Mark Sites of Mitochondrial Division","volume":"334","author":"JR Friedman","year":"2011","journal-title":"Science"},{"issue":"1","key":"pcbi.1011060.ref032","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1146\/annurev-genet-110410-132529","article-title":"Fusion and Fission: Interlinked Processes Critical for Mitochondrial Health","volume":"46","author":"DC Chan","year":"2012","journal-title":"Annu Rev Genet"},{"issue":"6","key":"pcbi.1011060.ref033","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1002\/bies.201400188","article-title":"What is the function of mitochondrial networks?","volume":"37","author":"H Hoitzing","year":"2015","journal-title":"BioEssays"},{"issue":"7859","key":"pcbi.1011060.ref034","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/s41586-021-03510-6","article-title":"Distinct fission signatures predict mitochondrial degradation or biogenesis","volume":"593","author":"T Kleele","year":"2021","journal-title":"Nature"},{"issue":"9","key":"pcbi.1011060.ref035","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1016\/j.bbabio.2008.05.001","article-title":"Mitochondrial fusion, fission and autophagy as a quality control axis: The bioenergetic view","volume":"1777","author":"G Twig","year":"2008","journal-title":"Biochim Biophys Acta BBA\u2014Bioenerg"},{"key":"pcbi.1011060.ref036","doi-asserted-by":"crossref","unstructured":"Sch\u00f6neberg J, Raghupathi G, Betzig E, Drubin D. 3D Deep Convolutional Neural Networks in Lattice Light-Sheet Data Puncta Segmentation. In: 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2019. p. 2369\u201372.","DOI":"10.1109\/BIBM47256.2019.8983012"},{"issue":"10","key":"pcbi.1011060.ref037","doi-asserted-by":"crossref","first-page":"101601","DOI":"10.1016\/j.isci.2020.101601","article-title":"MitoSegNet: Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology","volume":"23","author":"CA Fischer","year":"2020","journal-title":"iScience"},{"key":"pcbi.1011060.ref038","first-page":"491035","article-title":"The Allen Cell and Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images [Internet]","author":"J Chen","year":"2020","journal-title":"bioRxiv"},{"key":"pcbi.1011060.ref039","doi-asserted-by":"crossref","first-page":"e453","DOI":"10.7717\/peerj.453","article-title":"scikit-image: image processing in Python","volume":"2","author":"Walt S van der","year":"2014","journal-title":"PeerJ"},{"issue":"7","key":"pcbi.1011060.ref040","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"CA Schneider","year":"2012","journal-title":"Nat Methods"},{"key":"pcbi.1011060.ref041","article-title":"The igraph software package for complex network research","author":"G Csardi","year":"2006","journal-title":"InterJournal"},{"issue":"1","key":"pcbi.1011060.ref042","doi-asserted-by":"crossref","first-page":"17557","DOI":"10.1038\/s41598-019-53708-y","article-title":"Comparing methods for comparing networks","volume":"9","author":"M Tantardini","year":"2019","journal-title":"Sci Rep"},{"issue":"4","key":"pcbi.1011060.ref043","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1109\/TAES.2016.140952","article-title":"On implementing 2D rectangular assignment algorithms","volume":"52","author":"DF Crouse","year":"2016","journal-title":"IEEE Trans Aerosp Electron Syst"},{"key":"pcbi.1011060.ref044","doi-asserted-by":"crossref","first-page":"92","DOI":"10.3389\/fnana.2018.00092","article-title":"Automatic Mitochondria Segmentation for EM Data Using a 3D Supervised Convolutional Network","volume":"12","author":"C Xiao","year":"2018","journal-title":"Front Neuroanat"},{"key":"pcbi.1011060.ref045","article-title":"Mitochondrial dynamics and respiration within cells with increased open pore cytoskeletal meshes","author":"DH Jang","year":"2017","journal-title":"Biol Open"},{"issue":"4","key":"pcbi.1011060.ref046","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1016\/S0006-3495(91)82125-7","article-title":"Single particle tracking. Analysis of diffusion and flow in two-dimensional systems","volume":"60","author":"H Qian","year":"1991","journal-title":"Biophys J"},{"issue":"4","key":"pcbi.1011060.ref047","doi-asserted-by":"crossref","first-page":"041914","DOI":"10.1103\/PhysRevE.82.041914","article-title":"Mean square displacement analysis of single-particle trajectories with localization error: Brownian motion in an isotropic medium","volume":"82","author":"X. Michalet","year":"2010","journal-title":"Phys Rev E"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1011060","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T00:00:00Z","timestamp":1684108800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011060","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T06:17:53Z","timestamp":1702275473000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011060"}},"subtitle":[],"editor":[{"given":"Jason M.","family":"Haugh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,4,21]]},"references-count":47,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2023,4,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1011060","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1011060","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,21]]}}}