BioIO

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python

Documentation

See the full documentation on our GitHub pages site

Example Usage (see full documentation for more examples)

Install bioio alongside OME TIFF and OME ZARR plug-ins with pip (this example won't use the OME ZARR plug-in):

pip install bioio bioio-ome-tiff bioio-ome-zarr

from bioio import BioImage

# Get a BioImage object
img = BioImage("my_file.tiff")  # selects the first scene found
img.data  # returns 5D TCZYX numpy array
img.xarray_data  # returns 5D TCZYX xarray data array backed by numpy
img.dims  # returns a Dimensions object
img.dims.order  # returns string "TCZYX"
img.dims.X  # returns size of X dimension
img.shape  # returns tuple of dimension sizes in TCZYX order
img.get_image_data("CZYX", T=0)  # returns 4D CZYX numpy array

# Get the id of the current operating scene
img.current_scene

# Get a list valid scene ids
img.scenes

# Change scene using name
img.set_scene("Image:1")
# Or by scene index
img.set_scene(1)

# Use the same operations on a different scene
# ...

Issues

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