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, mountainssort, yass, ironclust, herdingspikes, hdsort, klusta...)

This interactive GUI offer several views that dynamically refresh other views. This allows us to very quickly check the strengths and weaknesses of any sorter output.

Contrary to other viewers (like phy), this viewer skips the tedious and long step of copying and reformatting the entire dataset (filtered signal + waveform + PCA) to a particular format or folder organisation. This gui is built on top of spikeinterface objects (Recording, Sorting, SortingAnalyzer) These 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 a local desktop app (old school!!). There is a web based viewer here.

Important note

The actual main branch is using the new SortingAnalyzer object from spikeinterface which is not released yet. You can expect some small bugs. If you want visualize the old WaveformExtractor from spikeinterface<=0.100.1 you need to go back to version spikeinterface-gui=0.8.0.

Launch

In order to use this viewer you will need to know a bit of spikeinterface

Step 1 : extract waveforms

You first need to is to get a SortingAnalyzer object with spikeinterface.

See help here

Note that:

• not all waveform snippets are extracted (See max_spikes_per_unit) only some of them
• this step is cached to a folder or zarr (and can be reloaded)
• this step can be run in parallel (and so is quite fast)
• optionally some extensionn can be computed (principal_components, spike_amplitudes, correlograms, ..) All extension will be rendered in an appropriated view.

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)


job_kwargs = dict(n_jobs=-1, progress_bar=True, chunk_duration="1s")

# make the SortingAnalyzer with some optional extensions
sorting_analyzer = si.create_sorting_analyzer(sorting, recording,
                                              format="binary_folder", folder="/my_sorting_analyzer",
                                              **job_kwargs)
sorting_analyzer.compute("random_spikes", method="uniform", max_spikes_per_unit=500)
sorting_analyzer.compute("waveforms", **job_kwargs)
sorting_analyzer.compute("templates")
sorting_analyzer.compute("noise_levels")
sorting_analyzer.compute("unit_locations", method="monopolar_triangulation")
sorting_analyzer.compute("isi_histograms")
sorting_analyzer.compute("correlograms", window_ms=100, bin_ms=5.)
sorting_analyzer.compute("principal_components", n_components=3, mode='by_channel_global', whiten=True, **job_kwargs)
sorting_analyzer.compute("quality_metrics", metric_names=["snr", "firing_rate"])
sorting_analyzer.compute("spike_amplitudes", **job_kwargs)

Step 2 : open the GUI

With python:

import spikeinterface_gui
# This creates a Qt app
app = spikeinterface_gui.mkQApp() 
# reload the SortingAnalyzer
sorting_analyzer = si.load_sorting_analyzer("/my_sorting_analyzer")
# create the mainwindow and show
win = spikeinterface_gui.MainWindow(sorting_analyzer)
win.show()
# run the main Qt6 loop
app.exec_()

Or simpler:

  import spikeinterface.widgets as sw
  sorting_analyzer = load_sorting_analyzer(test_folder / "sorting_analyzer")
  sw.plot_sorting_summary(sorting_analyzer, backend="spikeinterface_gui")

With the command line

sigui /path/for/my/sorting_analyzer

Install

For beginners or Anaconda users please see our installation tips where we provide a yaml for Mac/Windows/Linux to help properly install spikeinterface and spikeinterface-gui for you in a dedicated conda environment.

Otherwise,

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

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

From pypi:

pip install spikeinterface-gui

From source:

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 on top of spikeinterface.