gks2p_preprocess

---

This code uses modified suite2p that can be used in modules

Setting up

Installation

• create conda environment

  conda create --name gks2p python=3.9 pandas scipy spyder

• activate conda environment

  conda activate gks2p

• 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

  python -m pip install git+https://github.com/gkeliris/gks2p_preprocess.git@mecp2

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]'