Sholl analysis

[Nate]

Hi,

Any advice for performing Sholl analysis with Neuromantic?
Thanks.

Nate

[Nick Deems]

Hi, 

I imagine this is a shot in the dark (considering that you posted this 9 years ago...). Any chance you figured out sholl analysis using neuromantic files?

[Ben Suter]

Hi Nick,
You should be able to try various basic analysis by uploading the SWC
files from Neuromantic to the online version of L-Measure, but I
haven't tried this myself in a several years:
http://cng.gmu.edu:8080/Lm/Lmeasure.html
http://cng.gmu.edu:8080/Lm/

However, I personally take a different approach and don't use Scholl
analysis. Read on if interested:

For some brain areas, it is possible to align individual neurons in a
common, useful way. For neocortex, the pia (or a tangent of it) serves
as the x-axis, and the radial direction (across layers) as a y-axis.
In the hippocampus, there is a transverse and a longitudinal axis. For
pyramidal neurons in general, one can often define a primary axis
based on the apical trunk (manually, or by PCA). If you have a
systematic way of aligning your neurons, then instead of Scholl
analysis, I recommend a grid-based density analysis. You'll get a 2D
or 3D heatmap of (dendritic or axonal) length density or area density.
These maps can easily be averaged across types of neurons, or across
treatment conditions, and can be compared across groups. You can also
extract 1D radial density plots, of course (e.g. Fig. 4G).

Have a look at the kind of data and figures we generated here (Fig. 4 and 7):
Suter BA, Shepherd GMG (2015). Reciprocal interareal connections to
corticospinal neurons in mouse M1 and S2. The Journal of Neuroscience
35:2959-2974.
https://www.jneurosci.org/content/35/7/2959

If you want to try it, we released the Matlab-based software as part
of the following paper. Don't hesitate to contact me if you run into
any questions or issues getting it to work with your Neuromantic
files:
Yamawaki N, Borges K, Suter BA, Harris KD, Shepherd GMG (2014). A
genuine layer 4 in motor cortex with prototypical synaptic circuit
connectivity. eLife, e05422+.

You might also find these free NeuronLand software tools useful,
mainly for converting between file formats, but you can also do some
conversions, scalings, etc.
http://neuronland.org/NL.html

Good luck,
Ben.

PS: Please cite me if you end up using the density map approach or software.

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