bffile

Modern Bio-Formats wrapper for python

Documentation 📖

https://imaging-formats.github.io/bffile/

Installation

pip install bffile

Usage

Quick Start

from bffile import BioFile
import numpy as np

with BioFile("tests/data/ND2_dims_p4z5t3c2y32x32.nd2") as bf:
    # Access OME metadata
    print(bf.ome_metadata)  # ome_types.OME object

    # Get lazy array for series 0 (no data loaded yet)
    arr = bf.as_array(series=0)
    print(arr.shape, arr.dtype)  # (T, C, Z, Y, X) shape

    # Index specific planes on-demand
    plane = arr[0, 0, 2]  # Only reads this plane
    roi = arr[:, :, :, 100:200, 50:150]  # Sub-regions

    # Materialize all data when needed
    full_data = np.array(arr)

    # Or use dask for lazy computation
    darr = bf.to_dask(series=0, chunks="auto")
    result = darr.mean(axis=2).compute()

For simple cases, use imread() to load a single series/resolution into memory:

from bffile import imread

# Read series0/resolution0 into numpy array
# series and resolution parameters are optional and default to 0
data = imread("image.nd2", series=0, resolution=0)  
print(data.shape, data.dtype)  # (T, C, Z, Y, X) array

Selecting Bio-Formats Version

Bio-Formats is downloaded at runtime (via jgo).

By default, it will download the latest ome:formats-gpl:RELEASE maven artifact. You can specify a different version by setting the BIOFORMATS_VERSION environment variable:

This variable accepts either a simple version string (e.g. 6.0.1) or a full maven coordinate (e.g. ome:formats-gpl:6.0.1 or ome:formats-bsd:7.3.1):

# Use Bio-Formats 6.0.1 (GPL-licensed)
export BIOFORMATS_VERSION="6.0.1"

# Use BSD-licensed Bio-Formats 7.3.1
export BIOFORMATS_VERSION="ome:formats-bsd:7.3.1"

To see the currently installed version of Bio-Formats, you can check the BioFile.bioformats_version static method:

from bffile import BioFile

print(BioFile.bioformats_version())  # e.g. "8.1.1"

and to see the full maven coordinate that was used:

from bffile import BioFile

print(BioFile.bioformats_maven_coordinate())  # e.g. "ome:formats-gpl:8.1.1"

[!NOTE] We test back to version 6.0.1, but older versions may also work. If you specifically need this code to work with an older version of bioformats, please open an issue.

Java Runtime

[!TIP] No manual Java installation required!

This package automatically downloads and manages the Java runtime using cjdk (via scyjava).

By default, scyjava uses Zulu JRE 11 (defined here). You can configure the Java version and/or vendor using environment variables:

# Use Adoptium JDK 17
export BFF_JAVA_VERSION=17
export BFF_JAVA_VENDOR=adoptium

# Use Temurin JDK 21
export BFF_JAVA_VERSION=21
export BFF_JAVA_VENDOR=temurin

Available vendors: zulu-jre, zulu, adoptium, temurin, and other vendors listed in cjdk

Java 8 Support

Bffile is not currently expected to work with Java 8, as jpype has deprecated support for Java 8 as of jpype version 1.6. If you do want to try with Java 8, you will minimally need to explicitly pin jpype<1.6. If this is an important use case for you, please open an issue to discuss Java 8 support.

License

Licensing is a bit complicated for this project, so please read carefully.

• All code in this bffile repository is licensed under the BSD-3-Clause License. You may use and distribute this code under the terms of the BSD-3-Clause License.
• However, a user who installs bffile from PyPI will, by default, end up with Java jars that are licensed under the GPL-2.0 License (read below). As such, this package is listed on PyPI as GPL-2.0-or-later.

When you run bffile for the first time, it will automatically download a number of Java jars (via jgo), each of which has its own license. By default, bffile downloads the ome:formats-gpl:RELEASE maven artifact.

• ome:formats-gpl is licensed under the GPLv2+ License

If you would like to use bffile without any GPL-licensed jars, you can instead opt into using ome:formats-bsd by setting the BIOFORMATS_VERSION environment variable:

BIOFORMATS_VERSION="ome:formats-bsd"

• ome:formats-bsd is licensed under the BSD-2-Clause License

If you need a package that defaults to BSD-licensed jars (and ships as BSD-3 on PyPI), open an issue to discuss a bffile-bsd variant.