Project: tridesclous (GitHub Link)

tridesclous-master
- .circleci
  - requirements_testing.txt
  - config.yml
- readthedocs.yml
- tridesclous
  - dip.py
  - signalpreprocessor.py
  - peeler_engine_testing.py
  - iotools.py
  - cataloguetools.py
  - online
    - onlinetools.py
    - onlinepeeler.py
    - onlinetraceviewer.py
    - onlinewindow.py
    - __init__.py
    - tests
      - test_onlinewindow.py
      - test_onlinepeeler.py
    - onlinewaveformhistviewer.py
  - metrics.py
  - peeler_engine_geometry.py
  - sawchaincut.py
  - datasource.py
  - peeler_cl.py
  - report.py
  - version.py
  - export.py
  - matplotlibplot.py
  - cleancluster.py
  - gui
    - icons
      - test_ressources.py
      - icons.qrc
      - make_ressources.py
      - png
        view-refresh.svg
        document-new.svg
        preferences-other.svg
        autocorrection.svg
        document-export.svg
        probe-geometry.svg
        document-open.svg
        kwrite.svg
        configure-shortcuts.svg
        document-save.svg
      - __init__.py
    - waveformhistviewer.py
    - gui_params.py
    - peelerwindow.py
    - similarity.py
    - ndscatter.py
    - spikelists.py
    - featuretimeviewer.py
    - crosscorrelogramviewer.py
    - baselist.py
    - gpuselector.py
    - peaklists.py
    - tools.py
    - mainwindow.py
    - cataloguewindow.py
    - cataloguecontroller.py
    - traceviewer.py
    - initializedatasetwindow.py
    - probegeometryview.py
    - test_gpuselector.py
    - __init__.py
    - pairlist.py
    - silhouette.py
    - tests
      - test_peelerwindow.py
      - test_gui_tools.py
      - test_initializedatasetwindow.py
      - test_cataloguewindow.py
      - test_mainwindow.py
      - test_probegeometryview.py
    - waveformviewer.py
    - isiviewer.py
    - myqt.py
    - peelercontroller.py
    - base.py
  - peeler_engine_geometry_cl.py
  - tools.py
  - labelcodes.py
  - cltools.py
  - probe_list.py
  - datasets.py
  - peakdetector.py
  - numba_tools.py
  - decomposition.py
  - pythran_tools.py
  - peeler.py
  - __init__.py
  - peeler_engine_classic.py
  - peeler_engine_base.py
  - cluster.py
  - tests
    - test_decomposition.py
    - test_report.py
    - test_cluster.py
    - test_autoparams.py
    - test_datasource.py
    - test_iotools.py
    - test_cltools.py
    - test_cleancluster.py
    - test_dip.py
    - test_cataloguetools.py
    - probe_list.py
    - test_catalogueconstructor.py
    - test_signalpreprocessor.py
    - test_peeler.py
    - test_peakdetector.py
    - test_metrics.py
    - test_tools.py
    - testingtools.py
    - test_datasets.py
    - test_waveformtools.py
    - test_dataio.py
    - test_matplotlibplot.py
    - test_importers.py
    - test_export.py
  - pruningshears.py
  - scripts
    - __init__.py
    - tdc.py
  - dataio.py
  - autoparams.py
  - importers.py
  - waveformtools.py
  - catalogueconstructor.py
  - peeler_tools.py
- LICENSE
- appveyor.yml
- setup.py
- example
  - example_locust_dataset.ipynb
  - example_olfactory_bulb_dataset.ipynb
  - online_demo.py
  - example_olfactory_bulb_dataset.py
  - example_kampff_dataset.py
  - online_low_level_demo.py
- README.md
- requirements.txt
- .gitignore
- doc
  - release_notes.rst
  - Makefile
  - make.bat
  - img
    - peeler_animation.gif
  - realtime.rst
  - api.rst
  - step_by_step.rst
  - overview.rst
  - important_details.rst
  - releases
    - 1.3.0.rst
    - 1.0.0.rst
    - 1.4.0.rst
    - 1.1.0.rst
    - 1.3.1.rst
    - 1.3.2.rst
    - 1.4.2.rst
    - 1.3.3.rst
    - 1.4.1.rst
    - 1.6.0.rst
    - 1.5.0.rst
    - 1.2.0.rst
  - script_for_figures
    - generate_peeler_sequence_example.py
  - launch.rst
  - index.rst
  - conf.py
  - catalogue_window.rst
  - requirements
  - parameters.rst
  - installation.rst

trisdesclous: spike sorting with a French touch.

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Authors: Christophe Pouzat and Samuel Garcia

documentation

The documentation is here: http://tridesclous.readthedocs.io/

overview

tris des clous is a very dishonest translation of spike sorting to French.

Pronouce it [tree day clue] in English.

The primary goal of tridesclous was to provide a toolkit to teach good practices in spike sorting techniques. Trideslcous is now mature and can be used to sort spike on tetrode up to neuropixel probe recorded dataset.

Tridesclous is both:

an offline spike sorter tools able to read many file format
a realtime spike sorting combined with pyacq

Main features

template matching based method
several alternative methods at several processing steps of the chain
Qt GUI for interactive exploration
a simple python API to use in a notebook or to build a custom pipeline
support for many data formats (Raw, Blackrock, Neuralynx, Plexon, Spike2, Tdt, OpenEphys, ...) via neo
hardware acceleration with opencl: both GPU and multicore CPU
smaller memory footprint
built-in sample datasets to try on
quite fast for tetrode datasets -- expect x30 speedup over real time on a simple laptop
multi-platform
open source based on a true open source stack

The forest of spike sorting tools is dense and tridesclous is a new tree. Be curious and try it.

Installation

http://tridesclous.readthedocs.io/en/latest/installation.html

Launch

http://tridesclous.readthedocs.io/en/latest/launch.html

Screenshots

Offline Catalogue Window

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offline Peeler Window

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Online Peeler in a pyacq.Node

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Status