initial data processing scripts and functions for wrangling open-ephys data formats to formats usable for a range of spike sorting solutions (e.g. *.dat for klustasuite or phy), and batch scripts for calling both data formatting functions, pre-processing this data (spike detection, waveform clustering), and then simple plotting and analysis tools. This set includes template 'parameters' and 'probe'files required for running klustasuite and/or phy and a small handful of dependent functions developed elsewhere for ease of use.
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matlab code to view continuous data before pre-processing with spike detection and clustering
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matlab code to convert .continuous and .kwik files to .dat files (including one dependent function for reading open-ephys headers shamelessly taken from open-ephys/analysis-tools) and do some light pre-processing including referencing to a common-average reference and/or large event deletion following highpass filtering to mitigate large acute sources of noise
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4 tetrode-based probe files for sorting 1 or 8-tetrode data (with 32ch layout according to new lab standard 32ch EIBs in addition to open-ephys standard 32ch EIB correctly and 'backwards') for use with spikedetekt and klustakwik
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16ch-based probe file for a single-shank 16ch silicone probe for use with spikedetekt and klustakwik
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parameters template file with parameters for both the new and old 'klusta/phy' versions of spikedetekt and klustakwik
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post-clustering spike-time and waveform shape extraction from klustaviewa/klustakwik .kwik and .kwx -for use with both old (pre 2016) and curent .kwik flies
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post spike-detection scripts for taking raw (filtered) spike times and waveforms in a format convenient for loading into MClust tetrode-based spike sorting
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batch file for pre-processing, detecting spikes, and clustering 'raw' data from a handful of directories with a single click
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simple plotting of spike waveforms across tetrodes for sorting validation, with adjustable bandpass filtering of waveforms
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additional batch files for moving or deleting extranious data (.AUX files) across all subdirectories
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event extraction from open-ephys *.event files, MED-PC 'text' files, and lab standard *.tst files
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matlab code to convert spikedetekt // klusta // phy output to plexon's offlinesorter for data validation via neuroexplorer .nex files