Monday, September 17, 2012

How to Build a Neuron: Shortcuts

So you want to build a neuron, but don't have the time to fill and stain it, digitally reconstruct it, or even to knit one.

Knitting Neuroscience from Knit a Neuron
Well you are in luck because a lot of scientists have collected a lot of data already and some of them are even willing to openly share their work. 

While it is great that people are willing to share their data, that willingness alone is not enough to actually make the data widely accessible (or searchable for that matter). To bridge the chasm, other scientists have developed databases and repositories.  These databases and repositories store large datasets and organize them in a searchable way. 

The first shortcut to building a neuron I will discuss is the Cell Centered Database (CCDB).

Sounds a little like "self-centered" but represents just the opposite: scientists willing to share their data with everyone

In 2003, Martone and colleagues created the CCDB as a repository for 2D, 3D, and 4D images of cells that could be downloaded and used by researchers around the globe. There is a ton of data here, protein stains, electron microscopy, and fluorescent confocal images just to name a few.  While you could do a lot with this kind of information, I am just going to give you one example of how it can be used as a major short cut in the process of building a neuron.

So say you want to make a model of a cerebellum purkinje cell, but you don't have the time or lab facilities to fill and stain your own neuron.  You could go to CCDB, type in 'purkinje neuron' in the search box and download whichever 3D image stack suits your fancy. 

example Purkinje neuron that I just got from CCDB

With this data you could go straight to step 2: reconstructing the neuron

But what if you don't have the time to digitally reconstruct the neuron?  We have already discussed how much time reconstructing a neuron can take, so it's pretty easy to see why you would want to bypass that step too. And in fact, there is a database for that!

Halavi et al (2008) developed as a repository for neural reconstructions. has almost 8,000 downloadable digital reconstructions of neurons, which as they say on the website represents over 200,000 hours of manual reconstruction time., for all your neural needs.

Similar to CCDB, Neuromorpho offers much more than just a shortcut for lazy computational modelers. It has such detailed information about each neuron that a whole project could be done simply by comparing neural characteristics of different cell classes or different species. 

But my job here is to tell you how you can use it as a shortcut to building a neuron.

Say you want to build a computational model of a CA1 Hippocampal Pyramidal Cell, but you don't want to stain it and you don't want to reconstruct it.  Well, just go to and click 'browse by brain region' and then on 'hippocampus'. Then look through the 1,000 hippocampal cells (organized by class) that have already been reconstructed for you...

Pyramidal cell in the Hippocampus from
...and pick your favorite. 

Then you can jump right on through to step 3. (coming soon)

ResearchBlogging.orgHalavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, & Ascoli GA (2008). NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics, 6 (3), 241-52 PMID: 18949582

Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, & Ellisman MH (2008). The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. Journal of structural biology, 161 (3), 220-31 PMID: 18054501

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