Thanks in advance,
Mike
UPDATE: I should clarify that I *have* been able to get access to my morphology by doing
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from neuron import gui
Moderator: hines
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from neuron import gui
In a word, don't. Take the time to examine the data. Look at the error messages and warnings that Import3D generates, and take them seriously. Beware orphan sections and trees. Examine the imported cell from the side (you know how to rotate a shape plot around the z axis?) to make sure you aren't dealing with a reconstruction that suffers from z axis drift or backlash. Check the diameter measurements to make sure that there aren't bottlenecks; also verify that there is a plausible range of diameter measurements (or are there no values < 1um?).vellamike wrote:I'm trying to import a morphology in swc format using NEURON as a python library. I've searched the documentation for quite a while but so far have failed. Can somebody point me to where in the documentation this is explained or tell me how to do it?
and it should be, because importation of morphometric data requires critical examination of what you're getting. Don't just accept it because it seems to work without spawning error messages.UPDATE: I should clarify that I *have* been able to get access to my morphology by doingand then using the Tools->Miscellaneous->Import3D followed by export->instantiate, but this is of course very time consumingCode: Select all
from neuron import gui
Well, when you've gotten to the stage of having a model, you're well past the morphometry importaton stage, aren't you? Presumably you have scrutinized the imported data, and you're happy with it, or you wouldn't have bothered to assign biophysical parameters and decided on a discretization strategy.if I want to load my model hundreds of times
That should work.vellamike wrote:I want to assign all biophysical information in Python, the reasons being that:
1. I use many python methods to automate setting biophysical data in different ways
2. I find this much more readable
3. I try and use NEURON as a Python library as much as I can, doing as little as I can in the GUI
So after I've completed step 3 in your Workflow description I'm exporting to a hoc file immediately.
The CellBuilder already has the ability to export xml--see its Management page--and you can also export a top-level model cell (one whose sections actually exist) to xml from the Model View tool2.Is there any thought being given to exporting as a neuroml file from cellbuilder?