Installation

Install an Anaconda distribution of Python – Choose Python 3.x and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.

  1. Download the suite2p repository from GitHub using Git: git clone https://github.com/MouseLand/suite2p

  2. Open an anaconda prompt / command prompt with conda for python 3 in the path

  3. Change the current directory to the suite2p folder: cd suite2p

  4. Run conda env create -f environment.yml

  5. To activate this new environment, run conda activate suite2p. Afterwards, You should see (suite2p) on the left side of the terminal line.

  6. Install suite2p into this environment: pip install suite2p

  7. Now run suite2p and you’re all set.

If you have an older suite2p environment you can remove it with conda env remove -n suite2p before creating a new one.

Note you will always have to run conda activate suite2p before you run suite2p. Conda ensures mkl_fft and numba run correctly and quickly on your machine. If you want to run jupyter notebooks in this environment, then also conda install jupyter.

To upgrade suite2p (package here), run the following in the environment:

pip install suite2p --upgrade

Common issues

If when running suite2p, you receive the error: No module named PyQt5.sip, then try uninstalling and reinstalling pyqt5

pip uninstall pyqt5 pyqt5-tools
pip install suite2p

If when running suite2p, you receive an error associated with matplotlib, try upgrading it:

pip install matplotlib --upgrade

If you are on Yosemite Mac OS, PyQt doesn’t work, and you won’t be able to install suite2p. More recent versions of Mac OS are fine.

The software has been heavily tested on Windows 10 and Ubuntu 18.04, and less well tested on Mac OS. Please post an issue if you have installation problems. The registration step runs faster on Ubuntu than Windows, so if you have a choice we recommend using the Ubuntu OS.

Dependencies