Wiki source code of LFPykit showcase

Last modified by ehagen on 2022/05/27 11:07

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4.2	5	= LFPykit showcase =
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6.1	7	Demonstration on how to run predictions using LFPykit ([[LFPykit.rtfd.io>>url:https://lfpy.rtfd.io/]], [[github.com/LFPy/LFPkit>>url:https://github.com/LFPy/LFPy]]) on the Collaboratory.
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6.1	9	The LFPykit module provides electrostatic models in a manner that facilitates forward-model predictions of extracellular potentials and related measures from multicompartment neuron models, but without explicit dependencies on neural simulation software such as NEURON ([[https:~~/~~/neuron.yale.edu>>https://neuron.yale.edu]], [[https:~~/~~/github.com/neuronsimulator/nrn>>https://github.com/neuronsimulator/nrn]]), Arbor ([[https:~~/~~/arbor.readthedocs.io>>https://arbor.readthedocs.io]], [[https:~~/~~/github.com/arbor-sim/arbor>>https://github.com/arbor-sim/arbor]]), and LFPy ([[https:~~/~~/LFPy.readthedocs.io>>https://LFPy.readthedocs.io]], [[https:~~/~~/github.com/LFPy/LFPy>>https://github.com/LFPy/LFPy]])
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11.4	11	To use this material, create a new (private) collab and clone [[https:~~/~~/github.com/LFPy/LFPykit>>https://github.com/LFPy/LFPykit]] into it.
	12	Running notebooks here may result in file permission errors.
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11.2	14	The LFPykit package can be installed as
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11.2	16	{{{!pip install . # or !pip install LFPykit}}}
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4.3	18	in a jupyter notebook. Different usage with LFPy, NEURON and Arbor are provided in different notebooks located in the examples directory. Missing packages resulting in ImportError and similar can usually be installed issuing
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	20	{{{!pip install <missing-package-name>}}}
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	22	which may require a kernel restart to take effect.
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	24	Using the Official EBRAINS Docker image in the Lab is recommended as LFPykit and neural simulators (Arbor, NEURON, LFPy) is preinstalled. For new notebooks/console sessions use the EBRAINS_experimental_release (or select this as a kernel and restart when opening notebooks).
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	32	= What can I find here? =
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	34	* Notice how the table of contents on the right
	35	* is automatically updated
	36	* to hold this page's headers
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	38	= Who has access? =
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	40	Describe the audience of this collab.
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	46	{{box title="Contents"}}
	47	{{toc/}}
	48	{{/box}}
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