multiple neurites

[Linda]

Hi Darren,

Thanks so much for this very useful tool. I've begun using it to do
some branching analysis on retinotectal axons. The trouble is, I
rarely am able to label just one axon-- usually I must take images of
two or three and trace each one. I have been able to do this in
Neuromantic, but can't figure out how to get the program to analyze
each neuron separately. I tried creating categories "axon1, axon2"
etc., and have successfully colored the axons different colors. Can I
do the statistical analysis without retracing each axon individually
in its own reconstruction?

Thanks again for the Freeware.

Linda

[Kerry]

Hi Linda,

I've used Neuromantic a lot so I thought I'd comment. How many
separate axons do you have? Are they each separate SWC (data) files?
If they're all in one big SWC file then I'd suggest manually splitting
them into separate files since I can't think of a program that could
know where one axon ends and another begins. Separating them is as
easy as disconnecting them (they must be connected somehow if they
are all one SWC file), which you can do easily in Neuromantic, and
just deleting all but one tree and saving under a different name, then
doing this for each axon.

If this results in less than say 10 axons you could always just load
each one of these files one at a time and run the analyses. If this
results in more you can use a program like L-Measure (
http://krasnow.gmu.edu/cn3/data-tools.html ) which allows you to load
multiple SWC files at once and perform very similar measures as
Neuromantic. This link doesn't seem to be working right now so try
googling L-Measure or I can email you a copy of the program if you
wish.

Another option is to change the type of each axon (e.g. make one axon
of apical dendrite type and another soma etc), and see if the analysis
separates different tree types, but I think just disconnecting them
and making each its own SWC file would be easiest.

Let me know if you have any questions regarding this.

Kerry