Optimizing single cells programmatically
Posted: Thu Feb 07, 2019 1:24 pm
Hi all,
I'm trying to adopt the Allen Institute's single-cell model creation workflow: https://www.nature.com/articles/s41467-017-02718-3
However, during the "passive fitting" stage of the process (i.e. determining the optimal capacitance and leak conductance for the model), they use NEURON's MultipleRunFitter tool with the GUI (in HOC). I would like to do this step entirely using Python as the interpreter. Here are the steps I need to perform (ideally in a Jupyter Notebook):
1) Create a passive model (import SWC file, insert leak channels)
2) Use MultipleRunFitter to fit the passive model to experimental data just like in the HOC tutorial https://www.neuron.yale.edu/neuron/stat ... tline.html
I found this ancient post using HOC that essentially does what I need to do: viewtopic.php?t=805
But not sure how to do it in Python.
Any help is appreciated! Thank you.
I'm trying to adopt the Allen Institute's single-cell model creation workflow: https://www.nature.com/articles/s41467-017-02718-3
However, during the "passive fitting" stage of the process (i.e. determining the optimal capacitance and leak conductance for the model), they use NEURON's MultipleRunFitter tool with the GUI (in HOC). I would like to do this step entirely using Python as the interpreter. Here are the steps I need to perform (ideally in a Jupyter Notebook):
1) Create a passive model (import SWC file, insert leak channels)
2) Use MultipleRunFitter to fit the passive model to experimental data just like in the HOC tutorial https://www.neuron.yale.edu/neuron/stat ... tline.html
I found this ancient post using HOC that essentially does what I need to do: viewtopic.php?t=805
But not sure how to do it in Python.
Any help is appreciated! Thank you.