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Changes for page LFPykit showcase

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

From version 11.1
edited by ehagen
on 2022/05/23 22:36
Change comment: Update collab owner property to ehagen
To version 11.2
edited by ehagen
on 2022/05/27 10:53
Change comment: There is no comment for this version

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8 8  
9 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]])
10 10  
11 -To use this material, create a new collab and clone [[https:~~/~~/github.com/LFPy/LFPykit>>https://github.com/LFPy/LFPykit]] into it. Then the Python module can be installed as
11 +To use this material, create a new collab and clone [[https:~~/~~/github.com/LFPy/LFPykit>>https://github.com/LFPy/LFPykit]] into it.
12 12  
13 -{{{!pip install . # or pip install LFPykit}}}
13 +The LFPykit package can be installed as
14 14  
15 +{{{!pip install . # or !pip install LFPykit}}}
16 +
15 15  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
16 16  
17 17  {{{!pip install <missing-package-name>}}}
18 18  
19 19  which may require a kernel restart to take effect.
22 +
23 +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).
20 20  )))
21 21  )))
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