morphology altered when Import3d exports to CellBuilder

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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DavidSwygart
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Joined: Mon Dec 03, 2018 6:50 pm

morphology altered when Import3d exports to CellBuilder

Post by DavidSwygart »

I have loaded an swc with the Import3d GUI. The morphology looks correct. I then export the cell to CellBuilder GUI. At this point, the morphology looks incorrect. The longest branch containing the soma and axon seems to split, leaving the soma on one side of the dendrites and the axon on the other side. What could be going wrong here?

Here is a link to images of the problem and my session file.
https://drive.google.com/drive/folders/ ... sp=sharing

ted
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Re: morphology altered when Import3d exports to CellBuilder

Post by ted »

Rotation around the y axis. You're looking at the same thing, but from different angles.

DavidSwygart
Posts: 11
Joined: Mon Dec 03, 2018 6:50 pm

Re: morphology altered when Import3d exports to CellBuilder

Post by DavidSwygart »

I don't think it is purely a view rotation problem. Notice the location of the soma. It is the very wide portion below the dendrites in Import3d. The soma then moves above the dendrites in CellBuilder, while the rest of the axon seems to split off below the dendrites.

I have rotated the images to better show the difference between shape plot and import3d.

ted
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Re: morphology altered when Import3d exports to CellBuilder

Post by ted »

Your bitmaps are looking down the Y axis onto the XZ plane (X axis horizontal, Z axis vertical, Y axis orthogonal to the plane of the image).

I can't comment about the original morphometric data without seeing it for myself. However, I can tell you that in the imported model, what you are probably calling the soma is called dend_0[0].

print secname()
returns
dend_0[0]

Two separate subtrees are attached to the 0.5 location of dend_0; their most proximal sections are dend_0[1] and dend_0[12].

objref ssec
ssec = new SectionList()
dend_0[0] ssec.children()
forsec ssec print secname()
returns
dend_0[12]
dend_0[1]

Confirmed by exporting the model cell from the CellBuilder to a hoc file and then examining the file to see

Code: Select all

proc celldef() {
  topol()
  . . .
}

create dend_0[27]

proc topol() { local i
  connect dend_0[1](0), dend_0(0.5)
  . . .
  connect dend_0[12](0), dend_0(0.5)
  . . .
"Well, I don't want all children of the soma to attach to the middle of the soma."

Sorry, that's what the CellBuilder does, on the presumption that the soma is usually small compared to the total extent of the cell (so cosmetics aren't much affected by where things are attached), and electrotonically very compact (so anything attached to any part of the soma might just as well be attached to the middle). To prevent that from happening, the process of collecting morphometric data from the cell should be done in a way that treats the soma as a chain of two or more separate sections, with each child neurite connected to a junction between two adjacent soma sections. If you have a good idea of where the child neurites should be attached, you might try exporting the unsatisfactory CellBuilder to a hoc file (I'd export it to a cell class template), then edit a copy of that hoc file so that you get what you want. If you just want the two child neurites to attach to opposite ends of the soma, the editing task would be very easy because no pt3d data would have to be changed--simply change the connect statements.

DavidSwygart
Posts: 11
Joined: Mon Dec 03, 2018 6:50 pm

Re: morphology altered when Import3d exports to CellBuilder

Post by DavidSwygart »

The error was due to connecting to the center of dend_0[0]. I did not specify which section was the soma. I just traced an image and exported the swc, never annotating any compartments. NEURON took the first section to be the soma and then connected later sections to its middle. The first section turned out to be a long stretch of axon and so attaching the next section to its middle caused problems. I was able to avoid this by creating a tiny initial section in my trace. Everything looks good now.

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