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))
(CellBody)
Code: Select all
) ; End of contour
Code: Select all
( -637.05 685.32 60.93 0.18 S13) ; 9, 1
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:
23.91
15.22
12.99
6.52
17.39
. . .
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.