page_title: Neuronal tracing
section_title: Methods
hierarchical_section_title: Neuronal tracing / Digital neuronal reconstruction and neuronal tracing / Methods
caption_attribution_description: English: Schematic illustration of digital tracing of a neuron's morphology 中文: 神经元形态三维重建
context_page_description: Neuronal tracing, or neuron reconstruction is a technique used in neuroscience to determine the pathway of the neurites or neuronal processes, the axons and dendrites, of a neuron. From a sample preparation point of view, it may refer to some of the following as well as other genetic neuron labeling techniques,
  Anterograde tracing, for labeling from the cell body to synapse;
  Retrograde tracing, for labeling from the synapse to cell body;
  Viral neuronal tracing, for a technique which can be used to label in either direction;
  Manual tracing of neuronal imagery.
  In broad sense, neuron tracing is more often related to digital reconstruction of a neuron's morphology from imaging data of above samples.
context_section_description: Neurons can be often traced manually either in 2D or 3D. To do so, one may either directly paint the trajectory of neuronal processes in individual 2D sections of a 3D image volume and manage to connect them, or use the 3D Virtual Finger painting which directly converts any 2D painted trajectory in a projection image to real 3D neuron processes. The major limitation of manual tracing of neurons is the huge amount of labor in the work.
  Automated reconstructions of neurons can be done using model (e.g. spheres or tubes) fitting and marching, pruning of over-reconstruction, minimal cost connection of key points, ray-bursting and many others. Skeletonization is a critical step in automated neuron reconstruction, but in the case of all-path-pruning and its variants it is combined with estimation of model parameters (e.g. tube diameters). The major limitation of automated tracing is the lack of precision especially when the neuron morphology is complicated or the image has substantial amount of noise.
  Semi-automated neuron tracing often depends on two strategies. One is to run the completely automated neuron tracing followed by manual curation of such reconstructions. The alternative way is to produce some prior knowledge, such as the termini locations of a neuron, with which a neuron can be more easily traced automatically. Semi-automated tracing is often thought to be a balanced solution that has acceptable time cost and reasonably good reconstruction accuracy. The open source software Vaa3D-Neuron, Neurolucida 360, Imaris Filament Tracer and Aivia all provide both categories of methods.
  Tracing of electron microscopy image is thought to be more challenging than tracing light microscopy images, while the latter is still quite difficult, according to the DIADEM competition. For tracing electron microscopy data, manual tracing is used more often than the alternative automated or semi-automated methods. For tracing light microscopy data, more times the automated or semi-automated methods are used.
  Since tracing electron microscopy images takes substantial amount time, collaborative manual tracing software is useful. Crowdsourcing is an alternative way to effectively collect collaborative manual reconstruction results for such image data sets.
caption: Schematic illustration of digital tracing of a neuron's morphology
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