Questions on import3d and export tools

[Eleftheria Pissadaki]

Dear Forum,

Help is needed on the 'import3d' and 'export' tool of Neuron.
Importing a 3d reconstruction in Neuron results to 5 cell builders.
These 5 different topologies correspond to the five different dendritic processes that start from soma.
Apparently, each one of these are conceived as separate cells.
However, I would like to transform the whole cell in one file.
Do you have any suggestions for how to transform it succesfully using import3d and export methods?
Can a soma contour (drawn in Neurolucida) be finally classified as soma section in this conversion?
I would like to further elaborate with the particular tool before use cvapp or neuronland converters.

Thank you very much you time,

Kind regards,

Eleftheria

[ted]

Importing a 3d reconstruction in Neuron results to 5 cell builders.
These 5 different topologies correspond to the five different dendritic processes that start from soma.
Apparently, each one of these are conceived as separate cells.

because the morphometric data file is broken--the dendritic trees are not connected to the soma. Fix that, and the file will import as a single cell.

Can a soma contour (drawn in Neurolucida) be finally classified as soma section in this conversion?

What do you mean by a "soma contour"? A single outline of the periphery of the soma? Or multiple stacked contours? It is my understanding that NEURON automatically recognizes and deals with both cases automatically.

[Eleftheria Pissadaki]

Dear Ted,
Thank you very much for your reply.
The reconstruction of the cell has been made by me and I have done some validity test to see how reliable it is.
As you may know, cell bodies in Neurolucoda are drawn as stacks of contours. To my knowledge and my lab fellows, we can't splice a dendrite to a contour in Neurolucida environment.
That is, dendrites can't connect to the soma.
Would it be effective, if I try to redraw somatic region as a 'neuron tracing' and then splice the new cell body to the dendrites?
Soma contour is the periphery of the body cell in different z coordinates in order to produce a 3d somatic representation. In my case, five contours have been used to reproduce somatic region.

Kind regards,

Eleftheria

[hines]

If dendrites end within the bounding box of the soma then they should connect to
the soma. If you send the file to michael dot hines at yale dot edu I'll try to diagnose why
it is not importing correctly.

[Eleftheria Pissadaki]

Thanks, it works perfectly!

Eleftheria

[ted]

That's good to know.

[hines]

My email comments consisted of

The translator does not understand "Cell Body" with the space. Change to
"CellBody" without the space.
Also order the contours so that the z value is either monotonically
increasing or decreasing.