bffile

Yet another Bio-Formats wrapper for python

Installation

pip install git+https://github.com/tlambert03/bffile

Install Java ...

This package requires that you have java installed.
[INSERT GUIDELINES HERE]

Usage

from bffile import BioFile

with BioFile("tests/data/ND2_dims_p4z5t3c2y32x32.nd2") as bf:
    print(bf.ome_metadata)  # ome_types.OME object
    print(bf.shape)  # shows full shape
    data = bf.to_numpy(series=1)
    print(data.shape, data.dtype)