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.

From PyPIFrom napari hubFrom the GitHub main branchBuild from the source

pip install cylindra[recommended] -U

If you are using venv from uv,

uv pip install cylindra[recommended] -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

Clone the repository. Install git and run:

git clone https://github.com/hanjinliu/cylindra

or manually download the repository as a ZIP file and extract it.

Compile Rust code. You will nedd to have Rust installed.

cd cylindra
pip install .[recommended]

For Windows, you may need to install the Visual Studio with the "Desktop development with C++" workload.

Avoid installing optional dependencies

The "recommended" option tells pip to install packages that works well. If you don't want all of these, you can manually select the dependencies.

• pip install cylindra ... minimum installation with only the essential dependencies.
• pip install cylindra[all] ... all optional dependencies for cylindra.
• pip install cylindra[recommended] ... all optional dependencies with recommended versions.

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