Extractors module¶

Overview¶

The extractors module allows you to load BaseRecording, BaseSorting, and BaseEvent objects from a large variety of acquisition systems and spike sorting outputs.

Most of the Recording classes are implemented by wrapping the NEO rawio implementation.

Most of the Sorting classes are instead directly implemented in SpikeInterface.

Although SpikeInterface is object-oriented (class-based), each object can also be loaded with a convenient read_XXXXX() function.

import spikeinterface.extractors as se

Read one Recording¶

Every format can be read with a simple function:

recording_oe = read_openephys(folder_path="open-ephys-folder")

recording_spikeglx = read_spikeglx(folder_path="spikeglx-folder")

recording_blackrock = read_blackrock(folder_path="blackrock-folder")

recording_mearec = read_mearec(file_path="mearec_file.h5")

Importantly, some formats directly handle the probe information:

recording_spikeglx = read_spikeglx(folder_path="spikeglx-folder")
print(recording_spikeglx.get_probe())

recording_mearec = read_mearec(file_path="mearec_file.h5")
print(recording_mearec.get_probe())

Read one Sorting¶

sorting_KS = read_kilosort(folder_path="kilosort-folder")

Read one Event¶

events_OE = read_openephys_event(folder_path="open-ephys-folder")

For a comprehensive list of compatible technologies, see Supported File Formats.

Lazy loading¶

An important concept is that all read_XXXX() functions are lazy. Traces are not read from disk; instead only the relevant metadata (e.g. channel_ids, sampling frequency, etc.) is.

The actual reading will be done on demand using the get_traces() method:

# opening a 40GB SpikeGLX dataset is fast
recording_spikeglx = read_spikeglx(folder_path="spikeglx-folder")

# this really does load the full 40GB into memory : not recommended!!!!!
traces = recording_spikeglx.get_traces(start_frame=None, end_frame=None, return_scaled=False)

Supported File Formats¶

Currently, we support many popular file formats for both raw and sorted extracellular datasets. Given the standardized, modular design of our recording and sorting extractors, adding new file formats is straightforward so we expect this list to grow in future versions.

Most formats are supported on top of NEO

Dependencies¶

The neo package is a hard dependency of SpikeInterface. So all formats handled by Neo directly will also be handled in SpikeInterface.

However, some formats are handled directly by SpikeInterface and need extra installation.

You can install all extractors’ dependencies with:

pip install spikeinterface[extractor]

Raw Data Formats¶

For raw recording formats, we currently support:

AlphaOmega read_alphaomega()
Axona read_axona()
BlackRock read_blackrock()
Binary read_binary()
Biocam HDF5 read_biocam()
CED read_ced()
EDF read_edf()
IBL streaming read_ibl_streaming_recording()
Intan read_intan()
MaxWell read_maxwell()
MCS H5 read_mcsh5()
MCS RAW read_mcsraw()
MEArec read_mearec()
Mountainsort MDA read_mda_recording()
Neuralynx read_neuralynx()
Neurodata Without Borders read_nwb_recording()
Neuroscope read_neuroscope_recording()
Neuroexplorer read_neuroexplorer()
NIX read_nix()
Open Ephys Legacy read_openephys()
Open Ephys Binary read_openephys()
Plexon read_plexon()
Plexon 2 read_plexon2()
Shybrid read_shybrid_recording()
SpikeGLX read_spikeglx()
SpikeGLX IBL compressed read_cbin_ibl()
SpikeGLX IBL stream read_streaming_ibl()
Spike 2 read_spike2()
TDT read_tdt()
Zarr read_zarr()

Sorted Data Formats¶

For sorted data formats, we currently support:

BlackRock read_blackrock_sorting()
Combinato read_combinato()
Cell explorer read_cellexplorer()
HerdingSpikes2 read_herdingspikes()
HDsort read_hdsort()
Kilosort1/2/2.5/3 read_kilosort()
Klusta read_klusta()
MClust read_mclust()
MEArec read_mearec()
Mountainsort MDA read_mda_sorting()
Neurodata Without Borders read_nwb_sorting()
Neuroscope read_neuroscope_sorting()
Neuralynx spikes read_neuralynx_sorting()
NPZ (created by SpikeInterface) read_npz_sorting()
Plexon spikes read_plexon_sorting()
Plexon 2 spikes read_plexon2_sorting()
Shybrid read_shybrid_sorting()
Spyking Circus read_spykingcircus()
Trideclous read_tridesclous()
Wave Clus read_waveclus()
YASS read_yass()

Dealing with Non-Supported File Formats¶

With recording and sorting objects, we hope that any user can access SpikeInterface regardless of the nature of their underlying file format. If you feel like a non-supported file format should be included in SpikeInterface as an actual extractor, please open an issue.