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blik

Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.

https://github.com/brisvag/blik

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary

Keywords

cryo-et napari numpy python teamtomo visualization

Keywords from Contributors

interactive distribution tensor mesh interpretability profiles sequences generic projection standardization
Last synced: 6 months ago · JSON representation

Repository

Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.

Basic Info
Statistics
  • Stars: 27
  • Watchers: 4
  • Forks: 8
  • Open Issues: 5
  • Releases: 29
Topics
cryo-et napari numpy python teamtomo visualization
Created over 5 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

logo

blik

DOI Paper DOI License PyPI Python Version CI codecov

blik showcase

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:

bash 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

Nightly build

If you'd like the most up to date blik possible, you can install directly from the main branch on github. This also uses napari main, 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]"

Basic Usage

From the command line: bash 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 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.

Widgets

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 new segmentation, a new manually-picked set of particles, or a new surface, sphere, or filament picking for segmentation, particle generation or volume resampling.
  • add to exp: add a layer to the currently selected experiment (just a shorthand for layer.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 surfaces, spheres and filaments:

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

References

If you use blik, please cite the repo on zenodo and the paper on Plos Biology: https://doi.org/10.1371/journal.pbio.3002447.

Owner

  • Name: Lorenzo Gaifas
  • Login: brisvag
  • Kind: user
  • Company: @gutsche-lab

PhD student at @gutsche-lab, doing computational stuff with cryo-ET data.

GitHub Events

Total
  • Create event: 5
  • Release event: 1
  • Issues event: 3
  • Watch event: 6
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 5
  • Pull request event: 5
Last Year
  • Create event: 5
  • Release event: 1
  • Issues event: 3
  • Watch event: 6
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 5
  • Pull request event: 5

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 577
  • Total Committers: 6
  • Avg Commits per committer: 96.167
  • Development Distribution Score (DDS): 0.227
Past Year
  • Commits: 12
  • Committers: 2
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.083
Top Committers
Name Email Commits
Lorenzo Gaifas b****g@g****m 446
Alister Burt a****t@g****m 119
dependabot[bot] 4****] 9
Robert Haase h****f 1
Ricardo Righetto r****o 1
Marten Chaillet 5****t 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 20
  • Total pull requests: 80
  • Average time to close issues: 7 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 8
  • Total pull request authors: 5
  • Average comments per issue: 2.15
  • Average comments per pull request: 0.55
  • Merged pull requests: 69
  • Bot issues: 0
  • Bot pull requests: 13
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: about 4 hours
  • Average time to close pull requests: 5 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • brisvag (11)
  • alisterburt (2)
  • rdrighetto (2)
  • elainehoml (1)
  • JoeBeton (1)
  • McHaillet (1)
  • kimdn (1)
  • dmichalak (1)
Pull Request Authors
  • brisvag (53)
  • dependabot[bot] (13)
  • alisterburt (11)
  • rdrighetto (2)
  • McHaillet (1)
Top Labels
Issue Labels
bug (3) enhancement (1)
Pull Request Labels
dependencies (13) enhancement (2) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 311 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 34
  • Total maintainers: 1
pypi.org: blik

Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.

  • Versions: 34
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 311 Last month
Rankings
Dependent packages count: 10.1%
Downloads: 11.6%
Average: 14.4%
Dependent repos count: 21.6%
Maintainers (1)
brisvag
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • jupyter-book >=0.12.1
  • sphinx_material *
.github/workflows/ci.yml actions
  • JasonEtco/create-an-issue v2 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • aganders3/headless-gui v1 composite
  • codecov/codecov-action v3 composite
  • peaceiris/actions-gh-pages v3 composite
  • softprops/action-gh-release v1 composite
  • tlambert03/setup-qt-libs v1 composite
pyproject.toml pypi
  • cryohub >=0.5.0
  • cryotypes >=0.2.0
  • dask *
  • einops *
  • magicgui >=0.4.0
  • morphosamplers >=0.0.5
  • numpy *
  • pandas *
  • scipy *