Lattice Lightsheet Analysis

napari-lattice

Napari plugin for analysing and visualizing lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.


    View project data

    License PyPI Python Version tests PyPI - Downloads napari hub

    This napari plugin allows deskewing, cropping, visualisation and designing custom analysis pipelines for lattice lightsheet data, particularly from the Zeiss Lattice Lightsheet. Support will eventually be for other types of data.

    Documentation

    Check the Wiki page for documentation on how to get started.


    LLSZ_overview

    Functions

    • Deskewing and deconvolution of Zeiss lattice lightsheet images
      • 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 h5 (BigDataViewer/BigStitcher) or tiff files

    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


    This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

    Contributing

    Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

    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.

    Version:

    • 0.2.4

    Release date:

    • 17 November 2022

    First released:

    • 19 July 2022

    License:

    • GPL-3.0

    Supported data:

    • Information not submitted

    Plugin type:

    Open extension:

    GitHub activity:

    • Stars: 4
    • Forks: 1
    • Issues + PRs: 9

    Python versions supported:

    Operating system:

    Requirements:

    • aicsimageio (>=4.9.1)
    • aicspylibczi (>=3.0.5)
    • dask
    • dask-image
    • dask[distributed]
    • magic-class (>=0.6.7)
    • magicgui
    • napari[all]
    • pyopencl
    • read-roi
    • gputools
    • pyclesperanto-prototype (>=0.18.4)
    • napari-aicsimageio (>=0.7.2)
    • napari-spreadsheet
    • napari-workflows
    • napari-workflow-inspector
    • npy2bdv
    • redlionfish
    • tifffile
    • fsspec (>=2022.8.2)

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