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napari-lattice

napari-lattice is a toolset for deskewing, deconvolving, cropping, visualising and building custom analysis pipelines for light-sheet microscopy data — with a particular focus on the Zeiss Lattice Lightsheet 7 (LLS7).

It works both as a napari plugin (GUI) and as a command line interface (lls-pipeline, powered by lls-core), so you can process data interactively on the desktop or headless on an HPC at scale. The processing pipeline is modular and parameter-driven — every step (deskew, deconvolution, cropping, workflows, output) is configurable, which is what lets napari-lattice adapt to different acquisition geometries.

Deskewing lattice lightsheet data

Beyond the Zeiss LLS7

Because the deskew is parameter-driven — you set the skew direction (X or Y), skew angle, and whether to apply the coverslip rotation — napari-lattice generalises beyond the Zeiss LLS7. The same pipeline deskews oblique plane microscopy (OPM) data from non-Zeiss systems in different configurations. See --no-coverslip-rotation for the OPM/SOPi (shear-only) deskew mode.

What it can do

  • Deskew and deconvolve lattice lightsheet data, with a focus on the Zeiss LLS7
  • Handle other skewed-acquisition geometries, including oblique plane microscopy (OPM), via configurable skew direction, skew angle and coverslip rotation
  • Flip the scan direction (Invert Scan Direction) for microscopes whose stage/galvo scans run opposite to the Zeiss LLS
  • Generate a deskewed maximum-intensity projection (MIP) on the fly, computed straight from the raw data without ever building the full deskewed volume — fast and memory-light for terabyte-scale acquisitions
  • Preview a deskewed image at a channel or timepoint of interest, without processing the whole volume
  • Crop and process only a small region of interest, including ROIs imported from Fiji's ROI Manager
  • Build custom image-processing pipelines with napari-workflows
  • Run deskewing, deconvolution and workflows from the terminal for batch/HPC processing
  • Save output as OME-Zarr, HDF5 (BigDataViewer/BigStitcher) or TIFF

Get started

  • Installation

    Install napari-lattice (GUI) or just the lls-core command line interface.

    Install

  • Napari Plugin

    Open the plugin, load your data, and deskew, deconvolve and crop from the GUI.

    Use the plugin

  • Command Line

    Run lls-pipeline for headless, scriptable and HPC batch processing.

    CLI reference

  • Python API

    Drive the processing pipeline directly from Python with LatticeData.

    Python usage

  • Workflows

    Chain custom analysis steps onto the deskewed image with napari-workflows.

    Build a workflow

  • Supporting Resources

    Preparing ROIs for cropping and other helpful references.

    Resources

Sample data

Sample lattice lightsheet data is available on Zenodo: https://doi.org/10.5281/zenodo.7117784

Citing

If you use napari-lattice in your work, please cite:

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.14776381

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, and made possible in part by a napari plugin accelerator grant from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.