Help page for contestant's of the "National graduate mathematics modeling contest of China"

 Due to heavy traffic to our website during the contest the website may shut down occasionally. We will do our best to stay on top of this and bring the website up again as soon as we can. We apologize for the inconvenience.

Listed below is a summary of the frequently emailed questions that NeuroMorpho.Org has received so far. In an attempt to help the contestants during the competition, we have created this page to answer your questions.

Neuronal reconstructions

This repository is a public NIH-sponsored neuroscience repository containing a growing collection (5673) of digital reconstructions of neuronal morphology from laboratories worldwide. In the process of neuronal reconstruction, neurites are semi-manually traced through the use of specialized computer software and represented as binary trees of branching cylinders (or truncated cones). Therefore, the radius reported is the radius of each compartment (cylinder or cone). Note that some of the neurons may have been partially reconstructed. Therefore, the reconstructions may not contain soma or axon or dendrite, etc. However, this does not mean that the neuron does not have these segments.

To access the data

• Click on the "Metadata" on the left hand side menu
• There are many categories that you can use for your search. For example you can select "Cell type"
• Select the type of cell you need from the drop down menu. If you don't see the cell type that you are looking for, it means we don't have it in our database
• Click "Hits from criteria". It will show you the number of cells available on our website matching your search criteria
• Click on "Summary" button. It will take you to a page with a list of the neurons available from your search

To visualize the data

To visualize the neurons, we use Cvapp application , which associates a color to each type generated by the data owners. In SWC format there is a non-enforced rule for types:

• Soma: type 1, associated color: White or if more than one point Red
• Axon: type 2, associated color: Gray
• Basal dendrite: type 3, associated color: Green
• Apical dendrite: type 4, associated color: Magenta

* Note that each archive and each file can have other types associated with additional info (ex. fiduciary axes, spines, and etc.), which could appear with other colors. Additional tools for visualization of swc files:

• Neuromantic
• Neuronland Neuron viewer

All three application are available online to download and are free.

Measurements Extraction

For extracting morphometric information we use L-Measure software. We have selected and extracted 21 morphological measurements for each reconstruction, which are posted online in neuron detail page. More information can be found at FAQ page. Note that L-Measure can compute more than just the 21 measurements we have selected.
If you would like to use this software or extract additional measurements this software is available for free. Again due to heavy traffic for L-Measure also, it is advisable to download the L-Measure standalone, instead of using it online. You may download L-Measure from L-Measure download page.
This software runs as a standalone (LM.zip). Un-zip this file in the same folder that has both the GUI (Lm.jar) and executable (Lm.exe) files. When you double click the jar or run "java -jar Lm.jar" in the command line, you will be able to see the GUI which allows you to select the functions and compute the measurements on the given set of input neurons. The output is generated in a file. More documentation is also available on the L-Measure home page, which explains all of this in detail. Please visit the following link to get more information about the measurement parameters: L-Measure help page or download a detailed document here:

Width, Height and Depth

There may be some small discrepancies between values computed by L-measure now and what is posted online in NeuroMorpho.Org. The older version of L-Measure computed width, height and depth after running the PCA analysis. This used to be the default setting to calculate the width, height and depth values until the last release. However, the latest version 4.1 which is currently available on the website does not compute PCA implicitly. Instead, it uses the original orientation of the given input neuron to compute the width, height and depth. In other words, the difference of X-min and X-max values is computed as width (considering the 95% of the x-values and eliminating the 2.5% on either ends for outliers). Similarly, the Y and Z axes apply to height and depth respectively. So, to reiterate, the current version computes the width, height and depth values without PCA by simply assuming X, Y and Z axes for width, height and depth respectively.

On the other hand, the option to measure them using PCA is also still available, but needs to be selected explicitly. In L-Measure select the width, height and depth functions in the function panel and check the PCA option and click the Go button. The values are now computed using PCA.

Since these are tree level functions, you should make note that there is only one value of width for the entire tree and in the L-Measure output the minimum, average and maximum columns have the same final result. The total_sum column should be disregarded for these three functions.

Width is the measure of total length of neuron in x-axis.
(minimum to maximum of the x-scale)
Height is the measure of total length of neuron in y-axis.
(minimum to maximum of the y-scale)
Depth is the measure of total length of neuron in z-axis.
(minimum to maximum of the z-scale)

Related publication

1. L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Scorcioni R, Polavaram S, Ascoli GA. Nature Protocols. 2008; 3 (5):866-76. (PMID: 18451794)

2. Donohue D., Ascoli G.: A comparative computer simulation of dendritic morphology. PLoS Comput. Biol. 4(5): e1000089 (2008).
Additional publications can be found here.
Select the article you require and enter your email address when prompted. A pdf of the article will be sent to the email address.

Also the following references are examples of neuron growth studies:

O'Rourke, N.A., Cline, H.T. & Fraser, S.E. (1994) Rapid remodeling of retinal arbors in the tectum with and without blockade of synaptic transmission.Neuron 12:921-934.

Cline, H.T., Witte, S. and Jones, K. (1996) Nanomolar lead stunts neuronal growth in a reversible manner. Proc. Natl. Acad. Sci. (USA). 93: 9915-9919.

Witte, S., Stier, H. and Cline, H.T. (1996) In vivo observations of the timecourse and distribution of morphological dynamics in retinal axon arbors. J. Neurobiology 31: 219-234.

Wu, G-Y. and Cline, H.T. (1998) Stabilization of dendritic arbor structure in vivo by CaMKII. Science 279: 222-226.