spikeinterface-gui 0.4.1

GUI for spikeinterface objects

spikeinterface-gui

GUI for spikeinterface objects without data copy.

This is a cross platform interactive viewer to inspect the final results and quality of any spike sorter supported by spikeinterface (kilosort, spykingcircus, tridesclous, moutainssort, yass, ironclust, herdinspikes, hdsort, klusta...)

This interactive GUI offer several views that dynamically refresh other views. This allow to very quickly check strenght and wikness of a sorter otuput.

Contrary to other viewers (like phy), this viewer skip the tedious and long step of copying and reformating the entire dataset (filetred signal + waveform + PCA) to a particular format or folder organisation. This gui is built on top of spike interface objects (Recording, Sorting, WaveformExtractor) Theses objects are "lazy" and retrieve data on the fly (no copy!). And contrary to phy, this is a view only tool : no manual curation at the moment (split/merge/trash have to be done outside).

This viewer internally use Qt (with PySide6, PyQT6 or PyQt5) and pyqtgraph. And so, this viewer is local desktop app (old school!!). There is a web based viewer work-in-progres here.

Launch

You will need this viewer only and only if you known a bit of spikeinterface

Step 1 : extract waveforms

You first need to "extract waveform" with spikeinterface See help here

Note that:

• not all waveforms snipet are extracted (See max_spikes_per_unit) only some of then
• this step is cached to a folder (and can be reloaded)
• this step can be run in parralel (and so quite fast)
• optionaly PCa can be compute and displayed

Example:

import spikeinterface.full as si
recording = si.read_XXXX('/path/to/my/recording')
recording_filtered = si.bandpass_filter(recording)
sorting = si.run_sorter('YYYYY', recording_filtered)
waveform_folder = '/path/for/my/waveforms'
we = si.extract_waveforms(
    recording_filtered, sorting, waveform_folder,
    max_spikes_per_unit=500,
    ms_before=1.5, ms_after=2.5,
    n_jobs=10, total_memory='500M',
    progress_bar=True,
)
# and optionally compute principal component
pc = si.compute_principal_components(we,
    n_components=5,
    mode='by_channel_local',
    whiten=True)

Step 2 : open the GUI

With python:

import spikeinterface_gui
# This cerate a Qt app
app = spikeinterface_gui.mkQApp() 
# reload the waveform folder
we = si.WaveformExtractor.load_from_folder(waveform_folder)
# create the mainwindow and show
win = spikeinterface_gui.MainWindow(we)
win.show()
# run the main Qt6 loop
app.exec_()

With the commend line

sigui /path/for/my/waveforms

Install

You need first to install one of this 3 packages (by order of preference):

• pip install PySide6
• pip install PyQt6
• pip install PyQt5

From pypi:

pip install spikeinterface-gui

From sources:

git clone https://github.com/SpikeInterface/spikeinterface-gui.git
cd spikeinterface-gui
pip install .

Author

Samuel Garcia, CNRS, Lyon, France

This work is a port of the old tridesclous.gui submodule of top of spikeinterface.