How to Link Sorted Data to Electrodes

The SortedRecordingConverter maintains proper linkage between sorted units and their corresponding recording channels in NWB files. It handles the critical relationship between Units and Electrodes tables by:

• Creating electrode table regions for each unit

• Maintaining electrode group and device relationships

• Mapping channel IDs to electrode indices correctly

This automated handling ensures proper provenance tracking in the NWB file, which is essential for interpreting and analyzing sorted electrophysiology data.

Basic Usage

Single Probe and Single Recording

This example demonstrates linking data from a single Neuropixel probe recorded with SpikeGLX and sorted with Kilosort.

The converter requires three components:

1. A recording interface (SpikeGLXRecordingInterface)

2. A sorting interface (KiloSortSortingInterface)

3. A mapping between unit IDs and their associated channel IDs

First, instantiate the interfaces:

from neuroconv import SortedRecordingConverter
from neuroconv.datainterfaces import SpikeGLXRecordingInterface, KiloSortSortingInterface

# Initialize interfaces
recording_interface = SpikeGLXRecordingInterface(
    folder_path="path/to/spikeglx_data",
    stream_id="imec0.ap"
)
sorting_interface = KiloSortSortingInterface(
    folder_path="path/to/kilosort_data"
)

Access channel and unit IDs through interface properties:

# Access channel IDs
print(recording_interface.channel_ids)
# Example output: ['imec0.ap#AP0', 'imec0.ap#AP1', 'imec0.ap#AP2', ...]

# Access unit IDs
print(sorting_interface.unit_ids)
# Example output: ['0', '1', '2', ...]

Define the mapping between units and channels:

unit_ids_to_channel_ids = {
    "0": ["imec0.ap#AP0", "imec0.ap#AP1"],  # Unit 0 detected on two channels
    "1": ["imec0.ap#AP2"],                   # Unit 1 detected on one channel
    "2": ["imec0.ap#AP3", "imec0.ap#AP4"],   # Unit 2 detected on two channels
    ...  # Map all remaining units to their respective channels
}

Note

Every unit from the sorting interface must have a corresponding channel mapping.

Create the converter and run the conversion:

converter = SortedRecordingConverter(
    recording_interface=recording_interface,
    sorting_interface=sorting_interface,
    unit_ids_to_channel_ids=unit_ids_to_channel_ids
)

nwbfile = converter.run_conversion(nwbfile_path="path/to/output.nwb")