blik

it means glance in Dutch

blik is a tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional napari viewer and the scientific python stack.

DISCLAIMER: this package is in development phase. Expect frequent bugs and crashes. Please, report them on the issue tracker and ask if anything is unclear!

Installation¶

You can either install blik through the napari plugin system, through pip, or get both napari and blik directly with:

pip install "blik[all]"

The [all] qualifier also installs pyqt5 as the napari GUI backend, and a few additional napari plugins that you might find useful in your workflow:

• napari-properties-plotter
• napari-properties-viewer
• napari-label-interpolator

Basic Usage¶

From the command line:

napari -w blik -- /path/to.star /path/to/mrc/files/*

The -w blik is important for proper initialization of all the layers. Keep the main widget open to ensure nothing goes wrong!

blik is just napari. Particles and images are exposed as simple napari layers, which can be analysed and manipulated with simple python, and most importantly other napari plugins.

Widget¶

The main widget has a few functions: