5 Preprocessing - theory

This presentation can be found here.

(it may be converted into a quarto page)

6 Raw data quality metrics

7 Preprocessing Steps

import spikeinterface.extractors as si_extractors
from viewephys.gui import EphysBinViewer

# This should be the path to the folder containing
# the data. On Windows, you may need to prepend
# r to the string e.g. r"C:\my\path"
path_to_data_folder = "data/pipeline-walkthrough"

recording = si_extractors.read_spikeglx(
    path_to_data_folder,
    stream_id="imec0.ap"
)

import spikeinterface.preprocessing as si_prepro

phase_shift_recording = si_prepro.phase_shift(recording)
filtered_recording = si_prepro.bandpass_filter(
    phase_shift_recording, freq_min=300, freq_max=6000
)
cmr_recording = si_prepro.common_reference(
    filtered_recording, operator="median"
)

# show in EphysBinViewer(
    {
        "raw": recording,
        "phase_shift": phase_shift_recording,
        "filtered": filtered_recording,
        "cmr": cmr_recording
    }
)

7.1 Bad channe ldetection

Insert this step into the above pipeline

7.2 Highpass spatial filter

Replace CMR with HSF above

7.3 Drift correction

run drift correction
how to inspect the outputs (very important)
driftmaps (can use driftplots)
add to viewephys

7.4 Whitening

Don’t need much on this but just show the huge affect this has on the data

TODO: would be cool to add an ‘attach overlay data’ to a viewer and it will show it as overlay on the wiggle

7.5 Note on what steps the sorting applies

run kilosort and turn off various settings