Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
See the full documentation on our GitHub pages site
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
# ...Bioio handles a variety of different image types through specific plug-ins. The bioio-dev supported plug-ins can be found within this registry.
| Plug-in | Extension | Repository |
|---|---|---|
| arraylike | ArrayLike | Built-In |
| bioio-czi | .czi | Repo |
| bioio-dv | .dv, .r3d | Repo |
| bioio-imageio | .jpg, .png, Full List | Repo |
| bioio-lif | .lif | Repo |
| bioio-nd2 | .nd2 | Repo |
| bioio-ome-tiff | .ome.tiff, .tiff | Repo |
| bioio-ome-tiled-tiff | .tiles.ome.tif | Repo |
| bioio-ome-zarr | .zarr | Repo |
| bioio-sldy | .sldy, .dir | Repo |
| bioio-tifffile | .tif , .tiff | Repo |
| bioio-tiff-glob | .tiff (glob) | Repo |
| bioio-bioformats | Full List | Repo |
Each reader plugin should closely follow the specification laid out in bioio-base. As such, it is likely common that reader plugins won't distribute their own documentation and users should instead review bioio_base.reader.Reader for API documentation for the underlying Reader API. We encourage plugin authors to publish their own documentation if they change or include new features into their published image readers.
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