Create a new environment, Python need to be >=3.7
conda create --name environmnent
Activate you envinronment
If you want to use spyder
conda install spyder=5
for spikeinterface installation
pip install spikeinterface[full]==0.93
for phy
pip install phy==2.0b1
For Mountainsor4 in spikeinterface
pip install mountainsort4
Create a new environment Python need to be be 3.6
conda create --name environmnentMS4 python=3.6
If you want to use spyder
conda install spyder=5
The install mountainsort package
conda install -c flatiron -c conda-forge mountainlab mountainlab_pytools ml_ephys ml_ms3 ml_ms4alg ml_pyms
Install spikeforest widgets
pip install spikeforestwidgets
Downloads the file named python and add it to the path
Click on the python icon in spyder to open pythonpathmanager click on add path and go to the downloads python file to add it
Activate the spikeinterface environment, you can run Readmdaspike.py (use f9 instead of run). For that you will need a raw.mda file (M*N array of channel by timestamps), a geom.csv file and params.json file, you can find example of geom and params in the master It will import the raw in a recording apply a bandpass filter, do the spike sorting with mountainsort pipeline then export to phy the result. You can use the phy GUI to visualise the result by typing in the kernel
!phy template-gui phy_MS/params.py
you will need to be in the directory where the file is created
Activate the environment that has mountainsort
You can run the MS4.py file
To visualise the result you can use the GUI from mountainlab
You can install qt-mountainview with
conda install -c flatiron -c conda-forge qt-mountainview
The command in kernel is :
!qt-mountainview --raw=./raw.mda --geom=./geom.csv --firings=./output2/ms4/firings.mda --samplerate=30000
If you run into the error
ImportError: cannot import name 'Selector' from 'phylib.io.array' (/home/genzel/anaconda3/envs/environmnent/lib/python3.9/site-packages/phylib/io/array.py)
Go to https://github.com/cortex-lab/phy Downloads the master and replace the phy file in /home/genzel/anaconda3/envs/environmnent/lib/python3.9/site-packages by the phy file in the master