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  • Institut de Neurosciences de la Timone (INT)
  • Marseille, France
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JuliaSprenger / spikesorters.md
Last active March 23, 2023 20:57

This is an (incomplete) list of spike sorting tools available for (extraction and) sorting of spiking data from electrophysiologal experiments.

Software Reference Method Last Release Documentation Language On/Offline Commercial/Free Operating System GUI
SpikeOMatic http://www.biomedicale.parisdescartes.fr/SpikeOMatic Gaussian Mixture Model, Dynamic Hidden Markov Model 2010 minimal R/C (?) offline free linux / windowns minimal
Klusta http://klusta.readthedocs.io/en/latest Automatic sorting ? 2016 yes Python / Cython offline Free - yes
Phy http://phy.readthedocs.io/en/latest/ >100.000 recording sites 2018 In progress Python offline Free - yes
Wave_Clus http://www2.le.ac.uk/departments/engineering/research/bioengineering/neuroengineering-lab/spike-sorting Unsupervised, Wavelet and superparam. clustering 2009 yes Matlab offline Free - yes
Plexon Offl
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JuliaSprenger / Create PyPi release
Last active September 27, 2019 14:02
Check tests and issues
Check docu is running
Update version number + commit
Create tag locally `git tag 1.x.x`
Push tag to remote `git push origin --tags`
Create dist `python setup.py sdist`
Test `dist/<package><version>` is pip installable
Check compatiblity with PyPi `twine check dist/<package><version>.tar.gz`
Test package on PyPiTest `twine upload --repository pypitest dist/<package><version>.tar.gz`
Test installability from PyPiTest `pip install -i https://test.pypi.org/simple/ <package> --pre --extra-index-url https://pypi.org/simple`
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JuliaSprenger / create_conda_env_w_gin-cli.md
Created December 22, 2020 12:04
create conda environment with gin-cli and git-annex

Setting a conda environment for gin including git-annex

To set up a recent version of the gin client together with a recent version of git-annex one can set up a conda environment that contains both. For this you need to

  1. create the environment with git-annex
ginenv=<my-environment-name>
conda create -n "$ginenv" -c conda-forge git-annex
conda activate $ginenv
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JuliaSprenger / remove_git-annex_history.md
Last active November 4, 2021 11:26
Remove git-annex history locally and remotely

How to remove the history from a git-annex repository.

Here we are reducing the commit log of git and git-annex branches to a single commit. The following lines assume the repository has only a single remote 'origin', on which the history of the commits will also be reduced to a single commit. Note: Don't change the history of publicly shared repositories as this will lead to in inconsistent histories between different local copies of the repository.

Resetting local branches to a single commit

Squashing the master branch git reset $(git commit-tree HEAD^{tree} -m "")