blik
Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
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 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:
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:
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
for segmentation or particle generationadd to exp
: add a layer to the currently selectedexperiment
(just a shorthand forlayer.metadata['experiment_id'] = current_exp_id
)surface
: process a previously pickedsurface picking
layer to generate a surface mesh or distribute particles on it for subtomogram averaging.
Version:
- 0.5.5
Last updated:
- 20 September 2023
First released:
- 15 June 2021
License:
- GPL-3.0
Supported data:
- Information not submitted
Plugin type:
GitHub activity:
- Stars: 17
- Forks: 4
- Issues + PRs: 4