Sorting

The sorters are one separate program, dspk-cli-sorter, which dspk sort runs. It’s separate because Kilosort4 and EMUsort are GPL-3.0, and nothing MIT or Apache-licensed links them.

dspk sorters install                    # this version's build, SHA-256 checked
dspk sort kilosort4 recording.bin -o sorted --format phy
dspk sort kilosort4 --help              # every setting and its default

Start with a short stretch, using --start-sec and --duration-sec, before committing to a whole recording. --runtime cuda picks the runtime, and adding --show-config to a command prints every setting with its value.

The probe comes from the recording when it carries one (SpikeGLX). Otherwise pass --probe or --probe-file.

Note

From Python, sorts run on a server through dspk.remote. The sorters aren’t bound in the Python package, so that the wheel stays MIT or Apache-2.0.

What you get

A sorting in the format you asked for. Every sorter’s units are labelled good or mua by their auto-correlogram, and scored with EMUsort’s composite score.

Open it in the app, or load it:

sorting = dspk.synapse.io.Sorting.load("sorted")
sorting.units()                # a row per unit
sorting.spike_train(3)

dspk-cli-sorter licenses prints each sorter’s licence and source.

Where it’s installed

The user data folder: ~/.local/share/dspk/sorters/<version>/ on Linux, ~/Library/Application Support/dspk/… on macOS and %LOCALAPPDATA%\dspk\… on Windows. DSPK_DATA_DIR moves it, and DSPK_CLI_SORTER_BIN names another build.

Each sorter has a page on what it does, how it works and how to tune it.