Ephys recordings#

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.

Load it — drag & drop#

Tip

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

On the start page, drag your ephys file and/or Kilosort folder (and optionally a video and/or audio file) onto the Drag & drop zone.
Click Load.

EthoGraph recognises a Kilosort folder by the spike_times.npy inside it, and reads the sample rate and channel count from the file header or params.py automatically — no output path and no questions for known formats. Raw binary (.dat / .bin / .raw) has no header; drop it together with its Kilosort folder so the metadata comes from params.py (see below).

Two ephys trace viewers#

Raw traces can be shown in either of two panels, added from ➕ Add panel (Shift+N) under the Ephys header.

	Neo (`stream`)	Ephys (Phy-like viewer)
Reads	Any Neo-supported format (table below)	Raw binary (`.dat` / `.bin` / `.raw`) + Kilosort folder
Strength	Wide format compatibility	Fast zooming across many channels, with Kilosort spike waveforms overlaid on the trace

The Phy-like viewer is inspired by phy.

Supported formats#

EthoGraph uses Neo to read files with recognised headers — sample rate, channel count, and dtype are extracted automatically. Raw binary files have no header, so they 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 carries multiple signal streams (e.g. amplifier vs auxiliary channels in Intan), each stream appears as its own Neo (stream) entry in the ➕ Add panel popup, so you can open them side by side in separate panels.

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. This is what backs the Phy-like viewer.

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 Phy-like viewer, with spike waveforms overlaid on the trace.

Ephys with multiple trials#

The native route is to align video to the recording system: neuroconv puts the video on the recorder’s clock and writes a session.nwb with trials. Without a sync line, pair the files into a session.nc instead and select the ephys file in the GUI as above.