Data and code associated with: napari-lattice: A user-friendly image processing tool for lattice light-sheet microscopy data

Neutrophil NETosis — lattice light-sheet imaging & analysis Code and data accompanying the manuscript napari-lattice: A user-friendly image processing tool for lattice light-sheet microscopy data. The pipeline deskews and crops lattice light-sheet (LLS) timelapse data with napari-lattice, segments neutrophil nuclei with an ilastik pixel classifier, and extracts morphological/intensity measurements with scikit-image regionprops. Record contents File / archive Size Description code.zip ~20 MB All code: environment spec, example notebooks, test data, and HPC pipeline scripts. 6h_timelapse-06(1).czi 35.1 GB Zeiss lattice light-sheet timelapse (6 h), SPY650-labelled neutrophil nuclei. 6h_timelapse-06(1)_MIP.czi 302 MB Max-intensity 2D projection of the raw LLS data. 6h_timelapse_1_ROIs.zip ~3 kB Fiji ROIs used to crop individual cells from the timelapse. Supplementary_opm_data.zip 3.7 GB Two oblique-plane-microscopy datasets (raw + deskewed) showing the deskewing pipeline generalises beyond LLS. Data structure record/ ├── README.md overview, install, and usage (start here) ├── code.zip │ └── code/ │ ├── README.md copy of this overview │ ├── environment.yml conda/mamba environment spec │ ├── data/ empty; copy the raw .czi / ROIs here for the HPC pipeline │ ├── examples/ runnable demo (no cluster / raw data needed) │ │ ├── test_entire_workflow.ipynb end-to-end segmentation + measurement demo │ │ ├── create_napari_workflow.ipynb how the napari-workflows .yml is built │ │ └── test_data/ three small 3D crops (+ mask) and their README │ └── hpc_scripts/ SLURM batch pipeline (run on a cluster) │ ├── workflow/ segmentation function, ilastik classifier, workflow .yml │ ├── crop_analysis/ deskew + crop + run the segmentation workflow │ ├── crop_deskew_only/ deskew + crop only │ ├── deskew_only/ deskew only │ └── benchmarking/ runtime/scaling benchmarks (ROI vs full-FOV) ├── 6h_timelapse-06(1).czi raw LLS timelapse ├── 6h_timelapse-06(1)_MIP.czi max-intensity projection ├── 6h_timelapse_1_ROIs.zip Fiji cropping ROIs └── Supplementary_opm_data.zip ├── brain_organoid/ 4×-expanded brain organoid, direct-view OPM (raw + deskewed + config) └── thy1_eGFP/ Thy1-GFP mouse brain, scanned oblique plane (SOPi) (raw + deskewed + config) Start with README.md. Software: Python 3.10, ilastik-core 1.4.1, lls_core 1.2.1 (see environment.yml).