ZarrSmith — microscopy I/O, OME-Zarr forging, and NGFF utilities

ZarrSmith is a Python package for reading microscopy datasets from multiple acquisition systems, building multiscale pyramids, writing OME-NGFF / OME-Zarr, and working with those datasets from Python, the command line and napari.

The rendered documentation is at embl-mif.github.io/zarrsmith.

What ZarrSmith does

• Microscope managers read Luxendo, Opera, SCAPE, Viventis, Zeiss, Evident (Olympus VSI) and OME-Zarr datasets into one lazy (Dask) API with a shared metadata schema. → Readers and conventions
• OME-Zarr writing: full export, empty datasets and groups, image and label region updates, any subset of the tczyx axes. → Python API
• Pyramids and subsetting: multiscale generation, cropping, channel reordering, metadata updates. → Python API
• Mosaics: raw tiles shown at their stage position and fused into one OME-Zarr image (3D or projection, one timepoint or a timelapse). → Mosaics
• Chromatic shift correction: the Z offset between channels measured on the sample itself, on the reference channel and timepoint you choose and applied to every timepoint, and a corrected copy with the same layout as the input. → Chromatic shift correction
• Command line: one-off and CSV-batch conversion, mosaic fusion and chromatic shift correction. → Command line
• Napari widgets: conversion with ROI selection, mosaic fusion, exploration of segmented objects (features plot linked with the viewer). → Napari plugin
• Output tuning: sharding, singleton axes, parallel writing, progress bars. → Advanced writing options

Installation

conda create -n zarrsmith python=3.12
conda activate zarrsmith
pip install zarrsmith

Optional extras:

pip install "zarrsmith[napari]"      # napari widgets
pip install "zarrsmith[notebooks]"   # Jupyter, to run the example notebooks
pip install "zarrsmith[dev]"         # tests and packaging
pip install "zarrsmith[docs]"        # documentation build
pip install "zarrsmith[all]"         # all of the above

Extras can be combined, e.g. pip install "zarrsmith[napari,notebooks]".

Installing from source, development installs, versioning and releases: Installation and versioning.

Quick start

import zarrsmith.microscope_manager as mm

source = mm.ViventisManager("path/to/Position_1")   # any microscope manager
source.build_pyramid(num_levels=3)
source.to_zarr("output.zarr")                       # NGFF v0.5 / Zarr v3

z = mm.ZarrManager("output.zarr")
z.visualize()                                       # open in napari

zarrsmith convert -i INPUT_PATH -m MICROSCOPE -z OUTPUT_ZARR
zarrsmith fuse -i ACQUISITION_FOLDER -z OUTPUT_ZARR -rds 4 8 8   # fuse raw tiles
zarrsmith chromatic-shift -i INPUT_ZARR -z OUTPUT_ZARR -r shift.json   # align channels in Z

Documentation

Getting started

Working with data

Interfaces

Reference

Help

For questions or bug reports, open an issue on GitHub, or contact the current maintainers.