Simple reading and writing classes for tiled tiffs using Bioformats.
Project description
BioFormats Input/Output utility (bfio 2.3.1-dev0)
This tool is a simplified but powerful interface to Bioformats using jpype for direct access to the library. This tool is designed with scalable image analysis in mind, with a simple interface to treat any image like a memory mapped array.
Docker containers with all necessary components are available (see Docker Containers section).
Summary
Installation
Setting up Java
Note: bfio
can be used without Java, but only the python
and zarr
backends will be useable. Only files in tiled OME Tiff or OME Zarr format can be
read/written.
In order to use the Java
backend, it is necessary to first install the JDK.
The bfio
package is generally tested with
JDK 8,
but JDK 11 and later also appear to work.
Installing bfio
The bfio
package and the core dependencies (numpy, tifffile, imagecodecs) can
be installed using pip:
pip install bfio
Additionally, bfio
with other dependencies can be installed:
pip install bfio[bioformats]
- Adds support for BioFormats/Java. See License for additional information.pip install bfio[zarr]
- Adds support for OME Zarrpip install bfio[all]
- Installs all dependencies.
Docker
labshare/polus-bfio-util:2.3.1-dev0
Ubuntu based container with bfio and all dependencies (including Java).
labshare/polus-bfio-util:2.3.1-dev0-imagej
Same as above, except comes with ImageJ and PyImageJ.
labshare/polus-bfio-util:2.3.1-dev0-tensorflow
Tensorflow container with bfio isntalled.
Documentation
Documentation and examples are available on Read the Docs.
Versioning
We use SemVer for versioning. For the versions available, see the tags on this repository.
Authors
Nick Schaub (nick.schaub@nih.gov, nick.schaub@labshare.org)
License
This project is licensed under the MIT License Creative Commons License - see the LICENSE file for details.
NOTE
Bioformats is licensed under GPL, and as a consequence so is the bioformats_jar
package. These packages and libraries are installed when using the bfio[bioformats]
option.
Acknowledgments
- Parts of this code were written/modified from existing code found in
tifffile
.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for bfio-2.3.1.dev0-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e62ad2bfac51cc69dfa2c21e542d4faae5c59e8a8804fc05d47f4b5506af57d5 |
|
MD5 | 18be8b03c0d9efce01944574288b42ec |
|
BLAKE2b-256 | 759815dab1391d12b20dade0f5a2a2f4f6bf68399bca3ebffb3acf6e356fd3b3 |