Installation

Please refer to the suite2p README for the latest up-to-date installation instructions.

Common issues

If you receive an issue with Qt "xcb", you may need to install xcb libraries, e.g.:

sudo apt install libxcb-cursor0
sudo apt install libxcb-xinerama0

There is also more advice here: https://github.com/NVlabs/instant-ngp/discussions/300.

If you are having issues with CUDA on Windows, or want to use Cuda Toolkit 10, please follow these instructions:

conda create -n suite2p pytorch=1.8.2 cudatoolkit=10.2 -c pytorch-lts
conda activate suite2p
pip install suite2p

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

pip uninstall pyqt5 pyqt5-tools
pip install pyqt5 pyqt5-tools pyqt5.sip

If you are having other issues with the graphical interface and QT, see some advice here.

If you have errors related to OpenMP and libiomp5, then try

conda install nomkl

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

pip install matplotlib --upgrade

If you receive the error: ImportError: _arpack DLL load failed, then try uninstalling and reinstalling scipy

pip uninstall scipy
pip install scipy

If you are on Yosemite Mac OS or earlier, PyQt doesn't work and you won't be able to use the graphical interface for cellpose. 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.

Dependencies

Suite2p relies on the following excellent packages (which are automatically installed with conda/pip if missing): - pytorch - numpy (>=1.20.0) - scipy - scikit-learn - natsort - tifffile - scanimage-tiff-reader - pyqtgraph - PyQt6 or PySide - superqt

Suite2p also optionally uses our anatomical segmentation tool Cellpose. In the GUI our tool Rastermap is used for visualization