Skip to content

Examples

End-to-end walkthroughs that combine the individual features into a complete analysis.

  • Oblique plane microscopy (OPM)

    Deskew non-Zeiss OPM/SOPi datasets by matching the acquisition geometry — coverslip rotation and scan-direction inversion — on two published example datasets.

    OPM example

  • MIPs and defining ROIs

    Generate a deskewed MIP straight from raw data with --save-mip, draw cropping ROIs on it in Fiji, and feed them back into a crop run.

    MIP walkthrough

  • Neutrophil NETosis (end-to-end)

    Crop, deskew and analyse a live-cell LLS7 timeseries of neutrophils — first in the plugin, then headlessly on the command line with parallel ROI processing.

    End-to-end example

  • HPC processing with SLURM

    Run the same pipeline on an HPC cluster as a single SLURM job, distributing many ROIs across workers that share one GPU.

    SLURM example

About the data paths

These examples are based on the neutrophil dataset from the napari-lattice manuscript. The raw data is not bundled with the docs, so the file paths below are illustrative placeholders — substitute your own paths. The commands and options themselves are accurate.