simple-zarr-server

A simple server for sharing zarr over HTTP.

Installation

You can install simple-zarr-server via pip:

pip install simple-zarr-server

Usage

CLI:

$ simple-zarr-server /dataset.zarr # or /dataset.n5, or /dataset.zip

Python API:

The python API is more flexible than the CLI, and can serve any zarr.Array, zarr.Group or np.ndarray.

Server

from simple_zarr_server import serve
import numpy as np
arr = np.random.rand(1024, 1024)
serve(arr)

Client

zarr-python

import zarr
from fsspec import get_mapper
store = get_mapper("http://localhost:8000") 
arr = zarr.open(store, mode='r')
# or 
import dask.array as da
arr = da.from_zarr("http://localhost:8000")

zarr.js

import { openArray } from 'zarr';
arr = await openArray({ store: 'http://localhost:8000' });

Advanced: Serving a remote pyramidal tiff as Zarr

Server

from napari_lazy_openslide import OpenSlideStore
from simple_zarr_server import serve
import zarr

store = OpenSlideStore('tumor_004.tif') # custom zarr store
grp = zarr.open(store)
serve(grp)

Client

import napari
import dask.array as da
import zarr
from fsspec import get_mapper

store = get_mapper("http://localhost:8000")
grp = zarr.open(store)
datasets = z_grp.attrs["multiscales"][0]["datasets"]
pyramid = [
    da.from_zarr(store, component=d["path"]) for d in datasets
]
with napari.gui_qt():
    napari.view_image(pyramid)

Contributing

Contributions are very welcome. Tests can be run with tox.

License

Distributed under the terms of the BSD-3 license, "simple-zarr-server" is free and open source software

Issues

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