Adding myelin to realistic morphology
Posted: Mon Jul 18, 2016 10:27 am
Hello,
I'm working with cortical cell models with realistic morphologies that include the axon and its collaterals, and I'm applying extracellular stimulation via e_extracellular (using the xtra mechanism written by Ted). As is, the cell models are unmyelinated, but I'd like to add myelin to their existing axon morphologies. The cell models I'm working with all have a single section between branch points, so that every section originates from a bifurcation and ends in a bifurcation or termination. For each section of the axon, I want to set the bifurcation point as a node of Ranvier, calculate the internodal length based on the diameter at some point and the internodal length:diameter ratio (e.g. 100), and add the appropriate number of myelinated internodal "sections" and nodes in between the beginning and end of the section. I can think of several approaches to implement this, but they all seem to have problems, so I was hoping to get some advice on the best approach or alternatives. It's important that I retain the 3d morphology for extracellular stimulation, so I want to avoid adding or removing sections in a way that would change the coordinates. But for assigning extracellular potentials, I believe I should only need the coordinates of the nodes, assuming the myelin is perfectly insulating (for now).
These are the ideas I've had so far and their associated problems:
1) Modify compartments within each section to make them myelinated or nodal.
Problem: node much shorter than compartment lengths (1 µm vs. ~20 µm), can't set length of individual compartments, and setting all compartments to 1 µm would be too computationally expensive.
2) Use only last coordinate of each section, set to node (L= 1 µm), and simulate myelin section before node by modifying axial resistance
Problem: segments have 2 axial resistors, so modifying Ra in this way adds a myelinated section of the same length before and after the segment
3) Collapse each each section into last coordinates and set to node, as in 2, but disconnect children, add myelin section before it, and reconnect section w/ its children. Iterate through tree.
Problem: I think this would change the geometry unless I was careful about retaining the coordinates of the segments and assigning them to the myelin correctly
I'm working with cortical cell models with realistic morphologies that include the axon and its collaterals, and I'm applying extracellular stimulation via e_extracellular (using the xtra mechanism written by Ted). As is, the cell models are unmyelinated, but I'd like to add myelin to their existing axon morphologies. The cell models I'm working with all have a single section between branch points, so that every section originates from a bifurcation and ends in a bifurcation or termination. For each section of the axon, I want to set the bifurcation point as a node of Ranvier, calculate the internodal length based on the diameter at some point and the internodal length:diameter ratio (e.g. 100), and add the appropriate number of myelinated internodal "sections" and nodes in between the beginning and end of the section. I can think of several approaches to implement this, but they all seem to have problems, so I was hoping to get some advice on the best approach or alternatives. It's important that I retain the 3d morphology for extracellular stimulation, so I want to avoid adding or removing sections in a way that would change the coordinates. But for assigning extracellular potentials, I believe I should only need the coordinates of the nodes, assuming the myelin is perfectly insulating (for now).
These are the ideas I've had so far and their associated problems:
1) Modify compartments within each section to make them myelinated or nodal.
Problem: node much shorter than compartment lengths (1 µm vs. ~20 µm), can't set length of individual compartments, and setting all compartments to 1 µm would be too computationally expensive.
2) Use only last coordinate of each section, set to node (L= 1 µm), and simulate myelin section before node by modifying axial resistance
Problem: segments have 2 axial resistors, so modifying Ra in this way adds a myelinated section of the same length before and after the segment
3) Collapse each each section into last coordinates and set to node, as in 2, but disconnect children, add myelin section before it, and reconnect section w/ its children. Iterate through tree.
Problem: I think this would change the geometry unless I was careful about retaining the coordinates of the segments and assigning them to the myelin correctly