Downloaded a zip file from NeuroMorpho that was supposed to contain a couple of "log files" and two morphology files: one that NeuroMorpho calls "Original" and another called "Standardized". Expanding the zip file revealed two morphology files, one called 2M3.asc (in NeuroLucida text i.e. "ASCII" format, presumably the original morphology data) and the other called 2M3.CNG.swc (presumably NeuroMorpho's "standardized" morphology data).
Next I ran nrngui and used Import3d to import 2M3.asc
This generated the following output from NEURON's hoc interpreter:
Code: Select all
5290 lines read
./2M3.asc problems
Main branch starting at line 176 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
Main branch starting at line 2522 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
Main branch starting at line 2707 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
Main branch starting at line 3541 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
Now, that sounds like a fairly clear statement of what to expect when viewing the resulting model cell in NEURON: the proximal ends of four branched structures (dendritic or axonal trees) will appear to be physically separated from the soma.
So there you are. The fault lies in the original morphometric data. Blame a lack of standardization across laboratories about how to deal with somas when collecting morphometric data from neurons (this has been a striking and chronic problem for decades).
I should mention that, in addition to printing the above messages, NEURON popped up a panel that displayed the message
2M3.asc: File translation problems. See the messages on the terminal
and offered a Continue button. Clicking on that button brought up a panel with a drag bar labeled "Possible root branch errors." This panel reported
"Default logical connection to nearest soma" (which in this case should probably be accepted)
but it also offered a way to override this default action: four checkboxes that could be used to connect each of the proximal ends to the 1 end of the "closest parent in the xy plane". I suspect that would not be the correct choice for this particular cellular morphology.
Yet another alternative would be to accept the "standardized" morphology by using the Impor3d tool to import 2M3.CNG.swc (this file is in the "CNG version" subdirectory)
Do that, and you'll see no warnings or panels--but you'll still get a model cell that looks peculiar because the proximal ends of the dendritic and axonal trees don't appear to originate from the soma. Again, that's the fault of the original morphometric data.
Final question: are the dendritic and axonal trees actually electrically connected to the soma? I set Ra to 100 ohm cm, cm to 1 uf/cm2, inserted no other membrane properties, and discretized the cell using the d_lambda rule (with d_lambda = 0.1), applied a 1 nA current step at the soma that started at t = 1 ms, and examined a false color Shape plot using NEURON's default color scale--and found that the entire cell became quite yellow within 150-200 ms, which indicates that all sections are indeed electrically connected to the soma.
Rotating the cell reveals a small amount of backlash artifact (slop) along the z axis--far from the worst I have seen. Checking diam3d values shows that the smallest and largest measurements are plausible (but I always wonder about the accuracy of values < 0.3 um).