{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T00:31:53Z","timestamp":1776040313021,"version":"3.50.1"},"publisher-location":"New York, NY","reference-count":41,"publisher":"Springer US","isbn-type":[{"value":"9781071639689","type":"print"},{"value":"9781071639696","type":"electronic"}],"license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024]]},"DOI":"10.1007\/978-1-0716-3969-6_11","type":"book-chapter","created":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T16:02:45Z","timestamp":1723478565000},"page":"145-177","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["3D Reconstruction of the Mitochondrial Network within the Neuronal Soma from SBF-SEM Volume Data"],"prefix":"10.1007","author":[{"given":"Jane","family":"Tweedy","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ross","family":"Laws","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Merces","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tracey","family":"Davey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy K.","family":"Reeve","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy E.","family":"Vincent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,8,13]]},"reference":[{"issue":"3","key":"11_CR1","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1016\/j.neuron.2017.09.055","volume":"96","author":"T Misgeld","year":"2017","unstructured":"Misgeld T, Schwarz TL (2017) Mitostasis in neurons: maintaining mitochondria in an extended cellular architecture. Neuron 96(3):651\u2013666","journal-title":"Neuron"},{"issue":"8","key":"11_CR2","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1080\/15548627.2015.1062203","volume":"11","author":"X-T Cheng","year":"2015","unstructured":"Cheng X-T, Zhou B, Lin M-Y, Cai Q, Sheng Z-H (2015) Axonal autophagosomes use the ride-on service for retrograde transport toward the soma. Autophagy 11(8):1434\u20131436","journal-title":"Autophagy"},{"issue":"6","key":"11_CR3","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109509","volume":"36","author":"J Faitg","year":"2021","unstructured":"Faitg J, Lacefield C, Davey T, White K, Laws R, Kosmidis S et al (2021) 3D neuronal mitochondrial morphology in axons, dendrites, and somata of the aging mouse hippocampus. Cell Rep 36(6):109509","journal-title":"Cell Rep"},{"key":"11_CR4","first-page":"e54214","volume":"113","author":"K Mukherjee","year":"2016","unstructured":"Mukherjee K, Clark HR, Chavan V, Benson EK, Kidd GJ, Srivastava S (2016) Analysis of brain mitochondria using serial block-face scanning electron microscopy. J Vis Exp 113:e54214","journal-title":"J Vis Exp"},{"issue":"1","key":"11_CR5","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/s41467-017-00274-4","volume":"8","author":"SN Chaudhari","year":"2017","unstructured":"Chaudhari SN, Kipreos ET (2017) Increased mitochondrial fusion allows the survival of older animals in diverse C. elegans longevity pathways. Nat Commun 8(1):182","journal-title":"Nat Commun"},{"issue":"11","key":"11_CR6","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/nrm2275","volume":"8","author":"SA Detmer","year":"2007","unstructured":"Detmer SA, Chan DC (2007) Functions and dysfunctions of mitochondrial dynamics. Nat Rev Mol Cell Biol 8(11):870\u2013879","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"1","key":"11_CR7","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/S0006-8993(02)03767-8","volume":"960","author":"T Kobayashi","year":"2003","unstructured":"Kobayashi T, Kuroda S, Tada M, Houkin K, Iwasaki Y, Abe H (2003) Calcium-induced mitochondrial swelling and cytochrome c release in the brain: its biochemical characteristics and implication in ischemic neuronal injury. Brain Res 960(1):62\u201370","journal-title":"Brain Res"},{"issue":"33","key":"11_CR8","doi-asserted-by":"publisher","first-page":"8306","DOI":"10.1523\/JNEUROSCI.2614-08.2008","volume":"28","author":"J Verburg","year":"2008","unstructured":"Verburg J, Hollenbeck PJ (2008) Mitochondrial membrane potential in axons increases with local nerve growth factor or semaphorin signaling. J Neurosci 28(33):8306\u20138315","journal-title":"J Neurosci"},{"issue":"3","key":"11_CR9","first-page":"603","volume":"12","author":"P Anglade","year":"1997","unstructured":"Anglade P, Vyas S, Hirsch EC, Agid Y (1997) Apoptosis in dopaminergic neurons of the human substantia nigra during normal aging. Histol Histopathol 12(3):603\u2013610","journal-title":"Histol Histopathol"},{"issue":"1","key":"11_CR10","doi-asserted-by":"publisher","first-page":"18725","DOI":"10.1038\/srep18725","volume":"6","author":"L Zhang","year":"2016","unstructured":"Zhang L, Trushin S, Christensen TA, Bachmeier BV, Gateno B, Schroeder A et al (2016) Altered brain energetics induces mitochondrial fission arrest in Alzheimer\u2019s disease. Sci Rep 6(1):18725","journal-title":"Sci Rep"},{"issue":"31","key":"11_CR11","doi-asserted-by":"publisher","first-page":"12937","DOI":"10.1073\/pnas.1103295108","volume":"108","author":"FH Sterky","year":"2011","unstructured":"Sterky FH, Lee S, Wibom R, Olson L, Larsson N-G (2011) Impaired mitochondrial transport and Parkin-independent degeneration of respiratory chain-deficient dopamine neurons in vivo. Proc Natl Acad Sci 108(31):12937\u201312942","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"11_CR12","doi-asserted-by":"publisher","first-page":"414","DOI":"10.5607\/en.2019.28.3.414","volume":"28","author":"J Park","year":"2019","unstructured":"Park J, Seo J, Won J, Yeo H-G, Ahn Y-J, Kim K et al (2019) Abnormal mitochondria in a non-human primate model of MPTP-induced Parkinson\u2019s disease: Drp1 and CDK5\/p25 signaling. Exp Neurobiol 28(3):414\u2013424","journal-title":"Exp Neurobiol"},{"issue":"1","key":"11_CR13","doi-asserted-by":"publisher","first-page":"10278","DOI":"10.1038\/s41598-020-67091-6","volume":"10","author":"J Okarmus","year":"2020","unstructured":"Okarmus J, Bogetofte H, Schmidt SI, Ryding M, Garc\u00eda-L\u00f3pez S, Ryan BJ et al (2020) Lysosomal perturbations in human dopaminergic neurons derived from induced pluripotent stem cells with PARK2 mutation. Sci Rep 10(1):10278","journal-title":"Sci Rep"},{"issue":"23","key":"11_CR14","doi-asserted-by":"publisher","first-page":"4515","DOI":"10.1093\/hmg\/ddr381","volume":"20","author":"MJ Calkins","year":"2011","unstructured":"Calkins MJ, Manczak M, Mao P, Shirendeb U, Reddy PH (2011) Impaired mitochondrial biogenesis, defective axonal transport of mitochondria, abnormal mitochondrial dynamics and synaptic degeneration in a mouse model of Alzheimer\u2019s disease. Hum Mol Genet 20(23):4515\u20134529","journal-title":"Hum Mol Genet"},{"issue":"4","key":"11_CR15","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1083\/jcb.135.4.883","volume":"135","author":"AF Davis","year":"1996","unstructured":"Davis AF, Clayton DA (1996) In situ localization of mitochondrial DNA replication in intact mammalian cells. J Cell Biol 135(4):883\u2013893","journal-title":"J Cell Biol"},{"issue":"5","key":"11_CR16","doi-asserted-by":"publisher","DOI":"10.1098\/rsob.200061","volume":"10","author":"C Lawless","year":"2020","unstructured":"Lawless C, Greaves L, Reeve AK, Turnbull DM, Vincent AE (2020) The rise and rise of mitochondrial DNA mutations. Open Biol 10(5):200061","journal-title":"Open Biol"},{"issue":"1","key":"11_CR17","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1006\/exnr.2000.7333","volume":"162","author":"PA Trimmer","year":"2000","unstructured":"Trimmer PA, Swerdlow RH, Parks JK, Keeney P, Bennett JP Jr, Miller SW et al (2000) Abnormal mitochondrial morphology in sporadic Parkinson\u2019s and Alzheimer\u2019s disease cybrid cell lines. Exp Neurol 162(1):37\u201350","journal-title":"Exp Neurol"},{"issue":"1","key":"11_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-27058-0","volume":"8","author":"D Little","year":"2018","unstructured":"Little D, Luft C, Mosaku O, Lorvellec M, Yao Z, Paillusson S et al (2018) A single cell high content assay detects mitochondrial dysfunction in iPSC-derived neurons with mutations in SNCA. Sci Rep 8(1):1\u201316","journal-title":"Sci Rep"},{"issue":"1","key":"11_CR19","doi-asserted-by":"publisher","first-page":"1800927","DOI":"10.1002\/advs.201800927","volume":"6","author":"S Bolognin","year":"2018","unstructured":"Bolognin S, Foss\u00e9pr\u00e9 M, Qing X, Jarazo J, \u0160\u010dan\u010dar J, Moreno EL et al (2018) 3D cultures of Parkinson\u2019s disease-specific dopaminergic neurons for high content phenotyping and drug testing. Adv Sci (Weinh) 6(1):1800927","journal-title":"Adv Sci (Weinh)"},{"key":"11_CR20","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.jneumeth.2016.01.008","volume":"262","author":"L Wiemerslage","year":"2016","unstructured":"Wiemerslage L, Lee D (2016) Quantification of mitochondrial morphology in neurites of dopaminergic neurons using multiple parameters. J Neurosci Methods 262:56\u201365","journal-title":"J Neurosci Methods"},{"issue":"21","key":"11_CR21","doi-asserted-by":"publisher","first-page":"4118","DOI":"10.1093\/hmg\/ddx299","volume":"26","author":"W Wang","year":"2017","unstructured":"Wang W, Yin J, Ma X, Zhao F, Siedlak SL, Wang Z et al (2017) Inhibition of mitochondrial fragmentation protects against Alzheimer\u2019s disease in rodent model. Hum Mol Genet 26(21):4118\u20134131","journal-title":"Hum Mol Genet"},{"issue":"2","key":"11_CR22","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/S0014-4886(03)00342-X","volume":"186","author":"DD Song","year":"2004","unstructured":"Song DD, Shults CW, Sisk A, Rockenstein E, Masliah E (2004) Enhanced substantia nigra mitochondrial pathology in human \u03b1-synuclein transgenic mice after treatment with MPTP111-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine. Exp Neurol 186(2):158\u2013172","journal-title":"Exp Neurol"},{"issue":"11","key":"11_CR23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0020329","volume":"2","author":"W Denk","year":"2004","unstructured":"Denk W, Horstmann H (2004) Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2(11):e329","journal-title":"PLoS Biol"},{"issue":"47","key":"11_CR24","doi-asserted-by":"publisher","first-page":"12101","DOI":"10.1523\/JNEUROSCI.3994-06.2006","volume":"26","author":"KM Harris","year":"2006","unstructured":"Harris KM, Perry E, Bourne J, Feinberg M, Ostroff L, Hurlburt J (2006) Uniform serial sectioning for transmission electron microscopy. J Neurosci 26(47):12101\u201312103","journal-title":"J Neurosci"},{"issue":"6","key":"11_CR25","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/nprot.2011.332","volume":"6","author":"AJ Bushby","year":"2011","unstructured":"Bushby AJ, P\u2019ng KMY, Young RD, Pinali C, Knupp C, Quantock AJ (2011) Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy. Nat Protoc 6(6):845\u2013858","journal-title":"Nat Protoc"},{"key":"11_CR26","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.micron.2014.01.009","volume":"61","author":"CJ Peddie","year":"2014","unstructured":"Peddie CJ, Collinson LM (2014) Exploring the third dimension: volume electron microscopy comes of age. Micron 61:9\u201319","journal-title":"Micron"},{"key":"11_CR27","first-page":"e62045","volume":"169","author":"JA Courson","year":"2021","unstructured":"Courson JA, Landry PT, Do T, Spehlmann E, Lafontant PJ, Patel N et al (2021) Serial block-face scanning electron microscopy (SBF-SEM) of biological tissue samples. J Vis Exp 169:e62045","journal-title":"J Vis Exp"},{"issue":"1","key":"11_CR28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1002340","volume":"14","author":"I Belevich","year":"2016","unstructured":"Belevich I, Joensuu M, Kumar D, Vihinen H, Jokitalo E (2016) Microscopy image browser: a platform for segmentation and analysis of multidimensional datasets. PLoS Biol 14(1):e1002340","journal-title":"PLoS Biol"},{"issue":"7","key":"11_CR29","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nmeth.2089","volume":"9","author":"CA Schneider","year":"2012","unstructured":"Schneider CA, Rasband WS, Eliceiri KW (2012) NIH image to ImageJ: 25 years of image analysis. Nat Methods 9(7):671\u2013675","journal-title":"Nat Methods"},{"issue":"1","key":"11_CR30","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1006\/jsbi.1996.0013","volume":"116","author":"JR Kremer","year":"1996","unstructured":"Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116(1):71\u201376","journal-title":"J Struct Biol"},{"key":"11_CR31","volume-title":"Amira software for life & biomedical sciences","author":"Lanika Solutions","year":"2021","unstructured":"Lanika Solutions (2021) Amira software for life & biomedical sciences. ThermoScientific, Bangalore"},{"key":"11_CR32","doi-asserted-by":"crossref","unstructured":"Sommer C, Straehle C, Koethe U, Hamprecht FA (eds) (2011) Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE international symposium on biomedical imaging: from nano to macro. IEEE","DOI":"10.1109\/ISBI.2011.5872394"},{"issue":"7","key":"11_CR33","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9(7):676\u2013682","journal-title":"Nat Methods"},{"key":"11_CR34","doi-asserted-by":"crossref","unstructured":"Kaynig V, Fuchs T, Buhmann JM (eds) (2010) Neuron geometry extraction by perceptual grouping in ssTEM images. 2010 IEEE computer society conference on computer vision and pattern recognition; 13\u201318 June 2010","DOI":"10.1109\/CVPR.2010.5540029"},{"key":"11_CR35","unstructured":"Liu T, Jurrus E, Seyedhosseini M, Ellisman M, Tasdizen T (eds) (2012) Watershed merge tree classification for electron microscopy image segmentation. Proceedings of the 21st International Conference on Pattern Recognition (ICPR2012); 11\u201315 Nov 2012"},{"issue":"4","key":"11_CR36","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1016\/j.celrep.2019.01.010","volume":"26","author":"AE Vincent","year":"2019","unstructured":"Vincent AE, White K, Davey T, Philips J, Ogden RT, Lawless C et al (2019) Quantitative 3D mapping of the human skeletal muscle mitochondrial network. Cell Rep 26(4):996\u20131009.e4","journal-title":"Cell Rep"},{"key":"11_CR37","unstructured":"Taubin G (ed) (1995) Curve and surface smoothing without shrinkage. Proceedings of IEEE international conference on computer vision. IEEE"},{"issue":"11","key":"11_CR38","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.tcb.2017.08.009","volume":"27","author":"AE Vincent","year":"2017","unstructured":"Vincent AE, Turnbull DM, Eisner V, Hajn\u00f3czky G, Picard M (2017) Mitochondrial nanotunnels. Trends Cell Biol 27(11):787\u2013799","journal-title":"Trends Cell Biol"},{"issue":"6","key":"11_CR39","doi-asserted-by":"publisher","first-page":"900","DOI":"10.4103\/1673-5374.184477","volume":"11","author":"E Trushina","year":"2016","unstructured":"Trushina E (2016) A shape shifting organelle: unusual mitochondrial phenotype determined with three-dimensional electron microscopy reconstruction. Neural Regen Res 11(6):900","journal-title":"Neural Regen Res"},{"key":"11_CR40","doi-asserted-by":"publisher","DOI":"10.1016\/j.pneurobio.2019.101696","volume":"183","author":"C Cal\u00ec","year":"2019","unstructured":"Cal\u00ec C, Agus M, Kare K, Boges DJ, Lehv\u00e4slaiho H, Hadwiger M et al (2019) 3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from serial block-face electron microscopy of juvenile rat. Prog Neurobiol 183:101696","journal-title":"Prog Neurobiol"},{"key":"11_CR41","unstructured":"Newcastle Brain Tissue Resource. Institute of Neuroscience, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL"}],"container-title":["Methods in Molecular Biology","Neuronal Morphogenesis"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-3969-6_11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T16:04:27Z","timestamp":1723478667000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-3969-6_11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"ISBN":["9781071639689","9781071639696"],"references-count":41,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-3969-6_11","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024]]},"assertion":[{"value":"13 August 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}