From an ephys recording#

Use this path for extracellular electrophysiology data, with optional Kilosort spike-sorting output.

At least one of: an ephys file or a Kilosort folder is required.

Ephys is a session-wide stream — the raw recording file is selected in the GUI rather than embedded in the session.nc. For datasets with multiple behavioural trials alongside ephys, see Ephys with multiple trials.

Steps#

Tip

Install EthoGraph if you haven’t already, then launch via shortcut or: conda activate ethograph && ethograph launch

In the I/O widget, click Create with own data — the wizard opens.

  1. Under Single trial, select: 5) Generate from ephys file and/or kilosort folder

  2. Click Next — the dialog opens

  3. Set Ephys file and/or Kilosort folder

  4. Optionally set Video file or Audio file

  5. Set Output path for the generated session.nc

  6. Click Generate .nc file

  7. The I/O widget auto-populates -> click Load

Dialog fields#

Field

Notes

Ephys file

See supported formats below

Kilosort folder

Auto-detected if kilosort4/ or kilosort/ exists next to ephys file

Ephys sampling rate

Auto-detected from file or params.py; set manually for raw binary

N channels

Auto-detected for known formats; set manually for raw binary

Video file

Optional

Video onset in ephys

Time offset (s) where video starts relative to ephys recording

Audio file

Optional

Audio onset in ephys

Time offset (s) where audio starts relative to ephys recording

Output path

Where to save the generated session.nc

Supported formats#

EthoGraph uses Neo to read files with recognised headers — sample rate, channel count, and dtype are extracted automatically. Raw binary files are handled via phylib and require a Kilosort folder.

Known formats (headers auto-detected)#

Extension(s)

System

.rhd, .rhs

Intan

.oebin

Open Ephys Binary

.ns1-.ns6, .nev, .nsx

Blackrock

.abf

Axon (pCLAMP)

.edf, .bdf

EDF/BDF

.vhdr

BrainVision

.smr, .smrx

Spike2 (CED)

.ncs, .nse, .ntt

Neuralynx

.plx, .pl2

Plexon

.rec

SpikeGadgets

.meta

SpikeGLX

.xdat

NeuroNexus

.tbk / .tev / .tsq / …

TDT

.trc

Micromed

.edr, .wcp

WinEDR / WinWCP

.nwb

NWB file

When a format supports multiple signal streams (e.g. amplifier vs auxiliary channels in Intan), the GUI lets you select the desired stream from a combo box.

Raw binary (.dat / .bin / .raw)#

Raw binary files produced by Kilosort carry no metadata. They are loaded via phylib using n_channels and sample_rate read from params.py. Use the Kilosort folder picker rather than the ephys file browser — EthoGraph resolves the .dat path from params.py internally.

Kilosort spike sorting output#

Point the GUI at a Kilosort output folder via the Kilosort folder picker in the Ephys tab.

Auto-detection: If a kilosort4/ or kilosort/ directory exists next to your ephys file, EthoGraph fills the field automatically on selection.

Expected files#

File

Required

Description

spike_times.npy

Yes

Sample indices of each spike

spike_clusters.npy

Yes

Cluster ID per spike

cluster_info.tsv

Yes

Per-cluster metadata (group, ch, depth, …)

params.py

Auto-created if missing

Sample rate, channel count, raw data path

channel_positions.npy

Yes

Probe site coordinates (x, y) in um

channel_map.npy

Yes

Site index -> hardware channel mapping

params.py#

params.py is a plain Python file written by Kilosort:

dat_path = r'C:\data\recording.dat'
n_channels_dat = 385
dtype = 'int16'
sample_rate = 30000.0
hp_filtered = False

EthoGraph reads dat_path, n_channels_dat, and sample_rate from it. If the file is missing or dat_path no longer points to a valid file, a dialog prompts for the values and writes a new params.py so the step is not repeated.

What gets loaded#

  • cluster_info.tsv — cluster groups, best hardware channel (ch), depth, firing-rate statistics. Both KSLabel (automatic Kilosort classification) and group (phy manual curation) are imported.

  • channel_positions.npy + channel_map.npy — probe geometry for the raster and probe-channel dialog.

  • The raw .dat file (from dat_path) — displayed in the trace panel via the phylib loader.

Ephys with multiple trials#

Ephys is session-wide. If you have separate video/audio files per trial, build a session.nc first (see Multi-trial setup), then select the ephys file separately in the I/O widget.