bioio-emd

A BioIO plugin for reading and writing .emd images. It follows the BioIO reader and writer plugin APIs so files can be opened through bioio.BioImage alongside other format plugins.

Reading .emd files

from bioio import BioImage
import bioio_emd

img = BioImage("file.emd", reader=bioio_emd.Reader)
img.data

Accessing metadata

Source axes are mapped onto TCZYX. Known names such as x, y, z, and thickness keep their spatial axes. A non-navigation axis, such as complex, becomes the channel axis. Remaining axes fill unused slots in the order T, C, Z, Y, X.

img.dims.order  # "TCZYX"
img.dims.T, img.dims.C, img.dims.Z, img.dims.Y, img.dims.X
img.channel_names
img.physical_pixel_sizes  # Z, Y, X in micrometers

img.metadata is the file metadata dictionary. Classic Berkeley EMD files include the root version and the microscope, sample, and user groups:

img.metadata["sample"]["material"]
img.metadata["microscope"]["voltage"]

Writing .emd files

from bioio.writers import EmdWriter

EmdWriter.save(image, "file.emd", dim_order="ZYX")