Thursday, August 30, 2012

How to Build a Neuron: Step 2

Recently we've discussed the first step in how to build a neuron. Today we will discuss step 2: reconstructing that stained cell.

Hippocampus CA1 Pyramidal neuron (from
There are a couple of ways that you turn an image (or image stack) of a neuron into a digital neuron file like the one pictured above.  Basically there is an easy way and a hard way.  The hard way is to reconstruct the neuron manually, where you literally trace the neuron by hand.  The easy way is to auto-trace the neuron.

In a recent Frontier's in Neuroinformatics article, Myatt et al. (2012) explain the hard to easy gradient in reconstruction methods.

  • "Manual (Camera lucida). Prisms are employed to visually overlay the microscope image onto a piece of paper, and the neuron is then traced by hand. Although primarily used for 2D tracings, 3D reconstructions can be derived from these with time consuming post-processing (Ropireddy et al., ).
  • Semi-manual (e.g., Neuron_Morpho, Neurolucida). Digital segments are added by hand through a software interface, typically sequentially, beginning at the soma, and working down the dendritic tree.
  • Semi-automatic [e.g., NeuronJ (Meijering et al., ; 2D reconstruction only) and Imaris (3D reconstruction)]. User interaction defines the basic morphology, such as identifying the tree root and terminations, but branch paths are traced by the computer
  • Fully automatic (e.g., Imaris, NeuronStudio; Rodriguez et al., , AutoNeuron add-on for Neurolucida). The entire morphology is extracted with minimal user-input. " (Myatt et al., 2012)

You may ask: "Why not just do it the easy way?" Good question.  It is actually surprisingly difficult to make a versatile program that can accurately reconstruct neurons.  So difficult in fact that in 2010 an open challenge was issued with a monetary prize for the best automatic reconstruction algorithm. Five teams competed in this DIADEM challenge and the results and process are explained in detail in a special issue of Neuroinformatics. (And in less detail in this HHMI press release)

automatic reconstructions of neurons (source)
Advances in automatic reconstruction are being made at an astounding pace, but most neural reconstructions are still being done in a semi-manual or semi-automatic way. 

If you are interested in reconstructing some neurons, you can download Neuromantic for free or Neurolucida for money. There is other reconstruction software available, summarized nicely in Myatt et al. 2012, but these are the two I am most familiar with. 

In the next edition of "How to Build a Neuron" I will tell you how you can completely skip step 1 (the staining of the neuron) and step 2 (the reconstruction of the neuron). 

For ease of access, the whole "How to Build a Neuron" series is archived.

© TheCellularScale

ResearchBlogging.orgMyatt DR, Hadlington T, Ascoli GA, & Nasuto SJ (2012). Neuromantic - from semi-manual to semi-automatic reconstruction of neuron morphology. Frontiers in neuroinformatics, 6 PMID: 22438842

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