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lls-core

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

https://github.com/bioimageanalysiscorewehi/napari_lattice

Science Score: 57.0%

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 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 11 committers (45.5%) from academic institutions
  • ✓
    Institutional organization owner
    Organization bioimageanalysiscorewehi has institutional domain (imaging.wehi.edu.au)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary

Keywords

deconvolution deskewing image-analysis-and-processing lattice lightsheet microscopy napari oblique-plane python zeiss
Last synced: 6 months ago · JSON representation

Repository

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

Basic Info
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 4
  • Open Issues: 31
  • Releases: 12
Topics
deconvolution deskewing image-analysis-and-processing lattice lightsheet microscopy napari oblique-plane python zeiss
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License Zenodo

README.md

napari-lattice

License PyPI Python Version tests PyPI - Downloads

This napari plugin allows deskewing, cropping, visualisation and designing custom analysis pipelines for lattice lightsheet data, particularly from the Zeiss Lattice Lightsheet. It also has a command line mode (CLI), lls-core, so you can run it without the GUI.

Documentation

Check the Docs website for documentation on how to get started.

Functions

  • Deskewing and deconvolution of Lattice Lightsheet data with a focus on the Zeiss LLS7
  • Ability to preview deskewed image at channel or timepoint of interest
  • Crop and process only a small portion of the image
  • Import ImageJ ROIs for cropping
  • Create image processing workflows using napari-workflows
  • Run deskewing, deconvolution and custom image processing workflows from the terminal
  • Files can be saved as ome zarr, h5 (BigDataViewer/BigStitcher) or tiff files
  • COmmand Line Interface (CLI) lls-core to run napari-lattice workflows on the HPC at scale

Key Features

Apply custom image processing workflows using napari-workflows.

Support will be added for more file formats in the future.

Sample lattice lightsheet data download: https://doi.org/10.5281/zenodo.7117784

Citing

Rajasekhar, P., Milton, M., Geoghegan, N., Haase, R., Rogers, K. L., & Whitehead, L. (2025). napari-lattice (v1.0.3). Zenodo. https://doi.org/10.5281/zenodo.14974337

Contributing

Contributions are very welcome. Please refer to the Development docs to get started.

License

Distributed under the terms of the [GPL-3.0 License] license, "napari_lattice" is free and open source software

Acknowledgment

This project was supported by funding from the Rogers Lab at the Centre for Dynamic Imaging at the Walter and Eliza Hall Institute of Medical Research. This project has been made possible in part by Napari plugin accelerator grant from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.

Thanks to the developers and maintainers of the amazing open-source plugins such as pyclesperanto, aicsimageio, dask and pycudadecon. Thanks in particular to the developers of open source projects: LLSpy and lls_dd as they were referred to extensively for developing napari-lattice. Thanks to the imagesc forum!

Issues

If you encounter any problems, please file an issue along with a detailed description.

Owner

  • Name: BioimageAnalysisCoreWEHI
  • Login: BioimageAnalysisCoreWEHI
  • Kind: organization
  • Email: bioimageanalysis@wehi.edu.au
  • Location: Australia

GitHub Events

Total
  • Create event: 16
  • Release event: 4
  • Issues event: 24
  • Watch event: 1
  • Delete event: 23
  • Issue comment event: 96
  • Push event: 89
  • Pull request review comment event: 10
  • Gollum event: 1
  • Pull request review event: 9
  • Pull request event: 35
Last Year
  • Create event: 16
  • Release event: 4
  • Issues event: 24
  • Watch event: 1
  • Delete event: 23
  • Issue comment event: 96
  • Push event: 89
  • Pull request review comment event: 10
  • Gollum event: 1
  • Pull request review event: 9
  • Pull request event: 35

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 380
  • Total Committers: 11
  • Avg Commits per committer: 34.545
  • Development Distribution Score (DDS): 0.132
Top Committers
Name Email Commits
PRADEEP\Pradeep p****r@g****m 330
Pradeep Rajasekhar r****p@w****u 12
Robert Haase h****f@u****m 10
Lachlan Whitehead l****w@g****m 7
Lachlan Whitehead w****d@w****u 5
Lachlan Whitehead w****d@s****u 5
dependabot[bot] 4****]@u****m 3
Johannes Müller 3****r@u****m 2
Nina Tubau Ribera t****n@w****u 2
Laura Žigutytė z****e@g****m 2
Lachlan Whitehead w****d@s****u 2
Committer Domains (Top 20 + Academic)
wehi.edu.au: 3 slurm-login02.hpc.wehi.edu.au: 1 slurm-login01.hpc.wehi.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 66
  • Total pull requests: 72
  • Average time to close issues: 5 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 9
  • Total pull request authors: 5
  • Average comments per issue: 1.88
  • Average comments per pull request: 4.11
  • Merged pull requests: 43
  • Bot issues: 0
  • Bot pull requests: 14
Past Year
  • Issues: 14
  • Pull requests: 31
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 17 days
  • Issue authors: 4
  • Pull request authors: 4
  • Average comments per issue: 2.86
  • Average comments per pull request: 2.94
  • Merged pull requests: 24
  • Bot issues: 0
  • Bot pull requests: 4
View more stats
Top Authors
Issue Authors
  • pr4deepr (33)
  • multimeric (21)
  • DrLachie (4)
  • emmageddon-wehi (2)
  • brevid (2)
  • cyrfav (1)
  • kaitsull (1)
  • Eddymorphling (1)
  • cindy12-gao (1)
Pull Request Authors
  • multimeric (37)
  • pr4deepr (18)
  • dependabot[bot] (14)
  • DrLachie (10)
  • haesleinhuepf (2)
Top Labels
Issue Labels
enhancement (18) refactoring (8) bug (7) documentation (4) help wanted (1) github_actions (1) low_priority (1)
Pull Request Labels
dependencies (14) github_actions (14) enhancement (1) refactoring (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 399 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 21
  • Total maintainers: 2
pypi.org: napari-lattice

Napari plugin for analysing and visualizing lattice lightsheet and Oblique Plane Microscopy data.

  • Versions: 17
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 48 Last month
Rankings
Dependent packages count: 6.6%
Downloads: 16.9%
Average: 19.6%
Stargazers count: 20.5%
Forks count: 23.2%
Dependent repos count: 30.6%
Maintainers (2)
TMiguelT bac_wehi
Last synced: 6 months ago
pypi.org: lls-core

Core functionality for analysing and visualizing lattice lightsheet and Oblique Plane Microscopy data.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 351 Last month
Rankings
Dependent packages count: 10.0%
Average: 33.2%
Dependent repos count: 56.4%
Maintainers (1)
bac_wehi
Last synced: 6 months ago

Dependencies

.github/workflows/test_and_deploy.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
  • tlambert03/setup-qt-libs v1 composite
.github/lint/action.yml actions
  • jakebailey/pyright-action v1 composite
core/pyproject.toml pypi
  • StrEnum *
  • aicsimageio >=4.6.3
  • aicspylibczi >=3.1.1
  • click *
  • dask *
  • dask [distributed]
  • fsspec >=2022.8.2
  • importlib_resources *
  • napari-workflows >=0.2.8
  • npy2bdv *
  • numpy <2
  • ome-types <0.6.0
  • pandas *
  • pyclesperanto_prototype >=0.20.0
  • pydantic >=1.10.17,<3
  • pyopencl *
  • pyyaml *
  • read-roi *
  • resource-backed-dask-array >=0.1.0
  • rich *
  • scikit-image *
  • tifffile >=2023.3.15,<2025.2.18
  • toolz *
  • tqdm *
  • typer *
  • typing_extensions >=4.7.0
  • xarray [parallel]
plugin/pyproject.toml pypi
  • StrEnum *
  • aicsimageio >=4.6.3
  • dask [distributed]
  • fsspec >=2022.8.2
  • importlib_resources *
  • lls_core *
  • magic-class >=0.7.5
  • magicgui <0.8.0
  • napari [all]>=0.4.11
  • napari-aicsimageio >=0.7.2
  • napari-workflow-inspector *
  • napari-workflows >=0.2.8
  • npy2bdv *
  • numpy <2
  • ome-types <0.6.0
  • psutil *
  • pyclesperanto_prototype >=0.20.0
  • pydantic *
  • qtpy *
  • rich *
  • typing_extensions >=4.7.0
  • xarray *