oldaicsimageio 0.6.6

A generalized scientific image processing module from the Allen Institute for Cell Science.

AICS Image library

The oldaicsimageio package is designed to provide an easy interface with CZI, OME-TIFF, and PNG file formats.

Level of Support

We are not currently supporting this code for external use, but simply releasing it to the community AS IS. It is used for within our organization. We are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.

Development

See BUILD.md for information operations related to developing the code.

Usage

from oldaicsimageio import AICSImage

img = AICSImage("my_ome.tiff_or_tiff_or_czi")

# Get the image data as TCZYX
img.data

# Get channel information if you have an OME tiff
pixels = img.metadata.image().Pixels
channels = [pixels.Channel(i) for i in range(pixels.get_channel_count())]
channels = [{"name": c.get_Name(), "index": c.get_ID()} for c in channels]


# Note on channel id differences between oldaicsimageio.OMEXML and lxml.etree._Element:
        # Under lxml.etree._Element, Channel Id looks like the following: `'Channel:0'`
        # Where the single integer corresponds to the channel dimension index in image data.
        # Under oldaicsimageio, the same Channel Id looks like the following: `'Channel:0:0'`
        # Where it is the second of the two integers that corresponds to the channel dimension index in image data.
        # Regardless of structure, these can both be parsed as integers with the following:
        # `int(channel_id.split(":")[-1])`