zarr-tools

Convert nd2 to zarr

Installation¶

pip install zarr-tools

Usage¶

As command line¶

python -m zarr-tools file.nd2

This will produce the zarr dataset with default 5 steps of binning for xy dimensions.

As python module¶

import nd2
import zarr_tools

data = nd2.ND2File("input.nd2").to_dask()
zarr_tools.convert.to_zarr(
    data,
    channel_axis=1,
    path="output.zarr", 
    steps=4, 
    name=['BF','TRITC'], 
    colormap=['gray','green'],
    lut=((1000,30000),(440, 600)),
)