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

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

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

pip install"blik[all]"

The[all] qualifier also installspyqt5 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

If you'd like the most up to dateblik possible, you can install directly from themain branch on github. This also uses naparimain, so expect some instability!

pip install "git+https://github.com/brisvag/blik.git@main#egg=blik[all]"pip install "git+https://github.com/napari/napari.git@main#egg=napari[all]"

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. Always open the main widget open to ensure nothing goes wrong!

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

The main widget has a few functions:

• experiment: quickly switch to a different experiment id (typically, everything related to an individual tomogram such as volume, particles and segmentations)
• new: generate a newsegmentation, a new manually-picked set ofparticles, or a newsurface picking orfilament picking for segmentation, particle generation or volume resampling.
• add to exp: add a layer to the currently selectedexperiment (just a shorthand forlayer.metadata['experiment_id'] = current_exp_id)
• slice_thickness: changes the slicing thickness in all dimensions in napari. Images will be averaged over that thickness, and all particles in the slice will be displayed.

There are also widgets for picking of both surfaces and filaments.

• surface: process a previously pickedsurface picking layer to generate a surface mesh and distribute particles on it for subtomogram averaging, or resample a tomogram along the surface.
• filament: process a previously pickedfilament picking layer to generate a filament and distribute particles on it for subtomogram averaging, or resample a tomogram along the filament.

A paper preprint aboutblik is available on the bioRxiv:https://doi.org/10.1101/2023.12.05.570263.