surforama

a napari-based tool for using surfaces to explore volumetric data in napari

inspired by membranorama

installation

surforama requires the napari viewer. If you would like to install napari and surforama together in one line, you can use the following command:

pip install "surforama[napari]"

If you already have napari installed, you can directly install surforama in the same environment:

pip install surforama

usage

launch with demo data

If you'd like to test surforama out, you can launch surforama with demo data:

surforama --demo

launch without data

You can launch surforama using the command line interface. After you have installed surforama, you can launch it with the following command in your terminal:

surforama

After surforama launches, you can load your image and mesh into napari and get surfing!

launch with data

If you have an MRC-formatted tomogram and an obj-formatted mesh, you can launch using the following command:

surforama --image-path /path/to/image.mrc --mesh-path /path/to/mesh.obj

developer installation

If you would like to make changes to the surforama source code, you can install surformama with the developer tools as follows:

cd /path/to/your/surforama/source/code/folder
pip install -e ".[dev]"

We use pre-commit to keep the code tidy. Install the pre-commit hooks to activate the checks:

pre-commit install