Using Bio-Formats in Python
===========================
OME does not currently provide a Python implementation for Bio-Formats.
However, there are several options you can use to read images from Python via Bio-Formats:
AICSImageIO
-----------
The `AICSImageIO `_ project
includes support for Bio-Formats:
.. code-block:: python
from aicsimageio import AICSImage
cells = AICSImage('/path/to/my/cells.ome.tif')
import napari
napari.view_image(cells.xarray_data)
napari.run()
PyImageJ
--------
The `PyImageJ `_ project enables use of
`ImageJ2 `_, which includes the
`SCIFIO `_ library, which wraps Bio-Formats.
In this way, you can open Bio-Formats-supported formats as NumPy arrays:
.. code-block:: python
import imagej
ij = imagej.init('sc.fiji:fiji')
jcells = ij.io().open('/path/to/my/cells.ome.tif')
cells = ij.py.from_java(jcells)
import napari
napari.view_image(cells)
napari.run()
python-bioformats
-----------------
The :doc:`/users/cellprofiler/index` project has implemented a Python wrapper
around Bio-Formats used by the CellProfiler software which can be installed
using `pip`::
pip install python-bioformats
.. seealso::
https://pypi.org/project/python-bioformats
Source code of the CellProfiler Python wrapper for Bio-Formats