Getting started with bffile

bffile is a modern Bio-Formats wrapper for Python.

It exposes the full power of Bio-Formats in a clean Pythonic API backed by lazy data access.

Features

• Full lazy indexing and slicing (with no additional dependencis on dask/xarray/zarr) with bffile.LazyBioArray
• Custom zarr store presents files as complete multi-resolution OME-Zarr group
• Export to xarray DataArray with metadata-aware dimension and coordinate labels
• Export to Dask arrays for parallel and out-of-core computation

Installation

pip install bffile

Optional extras for zarr, xarray, and dask support, include:

pip install bffile[zarr,xarray,dask]

Quick start

import bffile

# load directly into memory
data = bffile.imread("path/to/file", series=0)

# or use lazy access to load only what you need
with bffile.BioFile("path/to/file") as biofile:
    # lazy series accessor
    lazy_array = biofile[0].as_array()
    # Load data into memory (T=0, C=1:4, Z=all, Y=100:200)
    data = lazy_array[0, 1:4, :, 100:200]

See usage for more details and examples.