This is a set of tools used for the semi-automated processing of raw ephys recording data. Things included here:
-spike extraction (spikedetekt) -automated spike sorting (klusta-3.0) -LFP downsampling and extraction (TODO) -synchronization of behavioral tracking data and ephys data (https://github.com/buzsakilab/buzcode)
INSTALL
cd ephys-processing-pipeline/installation
./install
Yes and enter to all queries
HOW TO RUN PIPELINE
run from within /ephys-processing-pipeline folder
python processRecordings.py /path/to/recording/folder numShanks
usage: processRecordings.py [-h] [-waitTime WAITTIME] [-numJobs NUMJOBS] [-cpuLimit CPULIMIT] [-repoPath REPOPATH] dataFolder numShanks
This function is designed to run in the background on a data processing machine. It constantly searches through a given directory [arg1] and starts extract, clustering, and other processing jobs
positional arguments: dataFolder the folder with all of your recordings in subdirectories numShanks number of shanks to process
optional arguments: -h, --help show this help message and exit -waitTime WAITTIME time (seconds) to wait before searching for more jobs [default = 300] -numJobs NUMJOBS number of jobs to run simultaneously [default = 4] -cpuLimit CPULIMIT cpu usage limit [default = 80] -repoPath REPOPATH location of ephys-processing repository