Soma stacks and the Import3d tool

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Soma stacks and the Import3d tool

Post by ted » Tue Mar 06, 2018 10:08 am

You may already know that the Import3d tool can handle Neurolucida morphometric data files in which the soma is defined by a stack of contours. A "soma stack" is a useful way to deal with complex soma shapes, because the soma volume and surface area of the resulting model will be more accurate (and the soma will look nicer in shape plots when you select the "Show Diam" style). However, the contours must be ordered monotonically according to depth (the z axis level). If they are out of sequence, importing the morphometric data can result in an obvious failure (breaking a single cell into two or more pieces that become separate "cells") or, worse yet, it can cause serious errors in soma volume and area that you may not notice but which will invalidate the resulting model cell.

It's easy to spot these errors by examining the contents of the morphometric data file. Make a copy of the file, then open the copy with a plain text editor. Soma contour data are typically near the beginning of the file. Each contour is specified by a block of text that starts something like this

Code: Select all

("Cell Body" ; I
  (Color RGB (255, 0, 128))
and ends with

Code: Select all

)  ;  End of contour
The data lines in a contour block will look like this

Code: Select all

  ( -637.05   685.32    60.93     0.18 S13)  ;  9, 1
The first three numbers on a line are the xyz coordinates of a point on the contour. The third number is the contour's z axis level; for any given contour, the z axis values will be identical or nearly identical.

Check each contour's z axis value, and make sure that the contours are arranged in an orderly manner, that is, bottom to top, or top to bottom. Here is the sequence of contour levels from a file I saw recently:
. . .
These contours are definitely not in a monotonic sequence. Even so, Import3d handled the file without complaint. Good? No, actually very bad. The surface area of the resulting model's soma was about 2520 um2. After the file was repaired by cutting and pasting the contour blocks in a monotonic sequence, the resulting model's soma had an area of only about 855 um2--three times smaller! That's a big difference, and it could have a significant effect on a model of a small cell like an interneuron.

If you are collaborating with someone who is generating morphometric data for you, it might be good to ask them to make sure to generate the contours in monotonic sequence along the z axis--either start at the bottom and work toward the top, or vice versa. But you, the modeler, are the ultimate user of the data, and you are responsible for deciding what will serve as the empirical basis of your models. Which means that you need to be aware of the problems that can affect morphometric data and know how to deal with them (either by fixing them or deciding to look for a better data set).

For other errors that can affect morphometric data, see Caveats about anatomically detailed model cells viewtopic.php?f=28&t=3862 in the Hot tips area of the forum.

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Re: Soma stacks and the Import3d tool

Post by Mohamed_Hisham » Fri Dec 07, 2018 10:10 pm

Hello ted, thanks for these great information.

I have a Neurolucida file (ASC), where the soma is constructed into multiple contours, the file is fine, the contours are monotonically increasing, so when importing the file to neuron I can see the whole structure including the soma.

but when exporting the morphology to the cell builder it opens multiple windows, every one has it's own soma attached to some branch of the tree. the ASC file has more than one "cellbody" contours. I wonder if there is a way to keep the soma structure intact, and would it be fine to have a multi-compartment as a soma.

Thank you very much

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