Convert nd2 to zarr
Project description
zarr-tools
Convert nd2 to zarr
Installation
pip install git+https://gitlab.pasteur.fr/aaristov/zarr-tools.git
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)),
)
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