title: KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons.
abstract: In axons, proper localization of proteins, vesicles, organelles, and other cargoes is accomplished by the highly regulated coordination of kinesins and dyneins, molecular motors that bind to cargoes and translocate them along microtubule (MT) tracks. Impairment of axonal transport is implicated in the pathogenesis of multiple neurodegenerative disorders including Alzheimer's and Huntington's diseases. To understand how MT-based cargo motility is regulated and to delineate its role in neurodegeneration, it is critical to analyze the detailed dynamics of moving cargoes inside axons. Here, we present KymoAnalyzer, a software tool that facilitates the robust analysis of axonal transport from time-lapse live-imaging sequences. KymoAnalyzer is an open-source software that automatically classifies particle trajectories and systematically calculates velocities, run lengths, pauses, and a wealth of other parameters that are characteristic of motor-based transport. We anticipate that laboratories will easily use this package to unveil previously uncovered intracellular transport details of individually-moving cargoes inside neurons.
authors: Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California.
authors: Sylvia
authors: S
authors: Neumann
authors: Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California.
authors: Romain
authors: R
authors: Chassefeyre
authors: Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California.
authors: George E
authors: GE
authors: Campbell
authors: Department of Molecular and Experimental Medicine, Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California.
authors: Sandra E
authors: SE
authors: Encalada
mesh_terms: D000818:Animals; D001370:Axonal Transport / Q000502:physiology; D001369:Axons / Q000378:metabolism / Q000502:physiology; D004398:Dyneins / Q000378:metabolism; D016547:Kinesins / Q000378:metabolism; D008870:Microtubules / Q000378:metabolism / Q000502:physiology; D019636:Neurodegenerative Diseases / Q000378:metabolism / Q000503:physiopathology; D009474:Neurons / Q000378:metabolism* / Q000502:physiology*; D015388:Organelles / Q000378:metabolism / Q000502:physiology; D012984:Software
chemical_list: D004398:Dyneins; D016547:Kinesins
keywords: 
  ImageJ
  ; axonal transport; kymograph; organelle; particle tracking; software tool