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.
You can install napari-sentinel-to-zarr via pip:
`pip install napari-sentinel-to-zarr`
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
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
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
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
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
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.
Distributed under the terms of the MIT license, "napari-sentinel-to-zarr" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.