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
# ...

Plug-in Registry

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-ins marked with * are community contributed and are maintained by external contributors.

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.

Writer Registry

BioIO supports a set of writer backends for exporting image data. The writer registry below lists maintained writer plug-ins.

Writer Installation and Usage

Writers will be installed with the respective plugin. Once installed they can be imported via bioio.writers. ex. bioio.writers<Writer Name>

import numpy as np
from bioio.writers import OmeTiffWriter # with bioio-ome-tiff installed

image = np.random.rand(10, 3, 1024, 2048)
OmeTiffWriter.save(image, "file.ome.tiff", dim_order="ZCYX")

Citation

If you use BioIO in your research, please cite the core bioio package via the DOI.

@software{bioio,
  author    = {BioIO Contributors},
  title     = {{BioIO}},
  url       = {https://github.com/bioio-devs/bioio},
  doi       = {10.5281/zenodo.22755965},
  year      = {2023},
}

For other citation formats, use the Cite this repository button at the top of this page (powered by the CITATION.cff file).

Note: BioIO's various plugins each carry their own license.

Issues

Click here to view all open issues in bioio-devs organization at once