Installation

For basic install instructions, look up the main github readme.

Built-in model directory

By default, the pretrained cellpose models are downloaded to $HOME/.cellpose/models/. This path on linux would look like /home/USERNAME/.cellpose/, and on Windows, C:/Users/USERNAME/.cellpose/models/. These models are downloaded the first time you try to use them, either on the command line, in the GUI or in a notebook.

If you’d like to download the models to a different directory, and are using the command line or the GUI, before you run python -m cellpose ..., you will need to always set the environment variable CELLPOSE_LOCAL_MODELS_PATH (thanks Chris Roat for implementing this!).

To set the environment variable in the command line/Anaconda prompt on windows run the following command modified for your path: set CELLPOSE_LOCAL_MODELS_PATH=C:/PATH_FOR_MODELS/. To set the environment variable in the command line on linux, run export CELLPOSE_LOCAL_MODELS_PATH=/PATH_FOR_MODELS/.

To set this environment variable when running cellpose in a jupyter notebook, run this code at the beginning of your notebook before you import cellpose:

import os
os.environ["CELLPOSE_LOCAL_MODELS_PATH"] = "/PATH_FOR_MODELS/"

Common issues

If you receive the error: Illegal instruction (core dumped), then likely mxnet does not recognize your MKL version. Please uninstall and reinstall mxnet without mkl:

pip uninstall mxnet-mkl
pip uninstall mxnet
pip install mxnet==1.4.0

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 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 having issues with the graphical interface, make sure you have python 3.7 and not python 3.8 installed.

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

cellpose relies on the following excellent packages (which are automatically installed with conda/pip if missing):