Installation

Create a virtual environment

Installing in a virtual environment is highly recommended. If you are using conda, you can create an environment with the command below, with "my-env" replaced with any names you'd like.

conda create -n my-env python  # create environment
conda activate my-env  # enter the virtual environment

Install Cylindra

Now, it's ready to install cylindra. Following command will install cylindra and all the relevant dependencies in the current virtual environment. Note that if you don't install from PyPI, you'll need git and rustup command.

From PyPIFrom napari hubFrom the GitHub main branchBuild from the source

pip install cylindra[all] -U

cylindra is available as a napari plugin. You can install it from the napari plugin manager.

1. Launch napari.
2. Click Plugins > Install/Uninstall plugins....
3. Type "cylindra" in the filter box. Click the "Install" button.

pip install git+https://github.com/hanjinliu/cylindra.git

git clone https://github.com/hanjinliu/cylindra
cd cylindra
pip install .[all]

Avoid installing optional dependencies

The "all" option tells pip to install everything that will be used in cylindra. If you don't want all of these, you can manually select the dependencies. The optional dependencies are:

• pyqt5 ... This is the default GUI backend. You can also use pyqt6 or pyside6.
• scikit-learn ... Conventional machine learning library. Princilple component analysis (PCA) and k-means clustering need this library.
• mrcfile ... A library for reading and writing MRC files. This is needed if you want to use MRC files.
• tifffile ... A library for reading and writing TIFF files. This is needed if you want to use TIFF files.

You can check if the installation succeeded by running cylindra -v.