# 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:

    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:

    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 CellProfiler project has implemented a Python wrapper around Bio-Formats used by the CellProfiler software which can be installed using pip:

    pip install python-bioformats

See also

https://pypi.org/project/python-bioformats

  Source code of the CellProfiler Python wrapper for Bio-Formats