Reconstruction cookbook?
Posted: Thu Dec 01, 2011 10:43 pm
Dear colleagues,
Does anybody know a good manual for reconstruction of anatomically detailed models? I am new in the field, and there are some immediate questions to the topic:
1) After I open the swc file in import3D and save it as Neuron hoc file, is it good enough to populate with ion channels and do simulations?
2) I guess, answer to Q.1 is NO in many cases. What are the necessary checks to do with the tree?
a) I know that soma must be non-zero length (happens in some swc files)
b) are 3-ple or 4-ple forks of processes allowed? Or only simple forks (--<) ? Any requirements from the cable equation solver?
c) check for loops?
d) ...?
Please, advice what are other common "quality-control" steps for making a good Neuron tree out of raw SWC file.
Thank you!
Does anybody know a good manual for reconstruction of anatomically detailed models? I am new in the field, and there are some immediate questions to the topic:
1) After I open the swc file in import3D and save it as Neuron hoc file, is it good enough to populate with ion channels and do simulations?
2) I guess, answer to Q.1 is NO in many cases. What are the necessary checks to do with the tree?
a) I know that soma must be non-zero length (happens in some swc files)
b) are 3-ple or 4-ple forks of processes allowed? Or only simple forks (--<) ? Any requirements from the cable equation solver?
c) check for loops?
d) ...?
Please, advice what are other common "quality-control" steps for making a good Neuron tree out of raw SWC file.
Thank you!