gks2p_preprocess

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This code uses modified suite2p that can be used in modules

Setting up

Installation

• create mamba environment

  mamba create --name [envname] python=3.9 pandas scipy

• activate mamba environment

  mamba activate [envname]

• install GAK:suite2p package directly from github

  python -m pip install "suite2p[gui] @ git+https://github.com/gkeliris/suite2p.git@gks2p"

• install scanreader

  pip3 install git+https://github.com/atlab/scanreader.git

• install the gks2p_preprocess repository from github (choose one)

  python -m pip install git+https://github.com/gkeliris/gks2p_preprocess.git@mecp2 (for MeCP2 datasets)

  python -m pip install git+https://github.com/gkeliris/gks2p_preprocess.git@lrn2p (for learning datasets)

  python -m pip install git+https://github.com/gkeliris/gks2p_preprocess.git@tepi (for temperature epilepsy)

• install FISSA

  pip install fissa

In case of problems / optional

• optional in case not working

  sudo apt-get install libegl1

  conda install pyqt

  pip uninstall PyQt6

  pip install PyQt5

• install scipy / pandas / spyder in case not installed with environment

  conda install pandas

  conda install scipy

  conda install spyder

• install VSCODE in case not already installed

  sudo snap install code --classic

• install CELLPOSE

  pip install 'cellpose[gui]'