Formats and probes

Recordings

On top of the core’s raw binary and Zarr, Synapse reads:

Format	Files
SpikeGLX	.bin or compressed .cbin, with its .meta
mtscomp	Compressed electrophysiology files
NWB	.nwb.zarr stores; each electrical series is a source

dspk open session.imec0.ap.bin       # its layout and read speed

Probes

A probe is the position of the site under every recording channel, in µm, with y as depth.

import dspk

probe = dspk.synapse.io.Probe.preset("neuropixels1")    # also neuropixels2, tetrode, utah, hdemg4x8, hdemg8x8
probe = dspk.synapse.io.Probe.grid(8, 8, pitch_um=8000.0)
probe = dspk.synapse.io.probe_of("session.imec0.ap.bin")   # what the file carries (SpikeGLX), or None

A probe file (.json: probeinterface or Kilosort 4) also says which channel each contact is wired to:

probe, map = dspk.synapse.io.read_probe_file("probe.json")

.mat probe files are refused. A probe follows a remap of its recording with probe.remap(map), and probe.depth_order() gives the map that sorts channels by depth. On the command line, dspk probe shows a layout and --write-map writes the map.

Sortings

A Sorting holds units with their spike trains, templates and quality metrics.

Format	How it’s chosen when saving
NWB /units, in a .nwb.zarr	Path ends in .nwb.zarr
.sorting.zarr	Any other .zarr path
Phy / Kilosort folder	Anything else

dspk convert in out converts between them.