napari-sentinel-to-zarr

Writer plugin for napari to save Sentinel tiffs into ome-zarr format

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

Installation

You can install napari-sentinel-to-zarr via pip:

`pip install napari-sentinel-to-zarr`

Usage

This package provides command-line utilities for:

• Processing raw Sentinel zips of a tile into multiscale zarr
• Processing interpolated “GapFilled” tif for that tile into zarr, rechunking along time axis
• Processing the zarr from step 2 into multiscale OME-zarr

Raw Zipped Images to Zarr

Install the latest version of napari using

pip install -U napari

Install napari-sentinel-to-zarr using

pip install napari-sentinel-to-zarr

Run sentinel-to-zarr zip-to-zarr path/to/tile/55HBU out/path/dir/55HBU.zarr

where path/to/tile/55HBU is a directory full of Sentinel zips

Interpolated Images to Zarr

Run sentinel-to-zarr interpolated-to-zarr path/to/interpolated/55HBU_GapFilled_Image.tif out/dir/Image.zarr

You can pass in optional arguments:

• --step-size - how many slices to convert at once. The default is 20 which will require ~5GB RAM. A larger step size means more slices can be loaded at once, and will speed up performance. A full image is typically ~175GB.
• --chunk-size - the chunk size of the resulting zarr. Default is 1024 which is typically considered a good option and provides good performance

Interpolated Zarr to Multiscale Zarr

Run sentinel-to-zarr zarr-to-multiscale-zarr path/to/interpolated/zarr out/path/interpolated_multiscale.zarr tilename

Where path/to/interpolated/zarr is the output file from step 2

You can pass in optional arguments

• --min-shape- the smallest pyramid level you wish to generate. Default is 1024px

Napari Plugin

This package also comes with a napari writer plugin which allows you to open the raw tiles directly by dragging one into a napari viewer, and saving out while you browse using File>Save Layers <<<<<<< HEAD

Stashed changes ======= fb66ae98f8a36fe3d90cd02f1892b326fc180b52

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 MIT license, "napari-sentinel-to-zarr" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.