Link AICSImage Object to Napari Layers
This release can be summed up by the new addition in the README:
You can access the
AICSImage
object used to load the image pixel data and
image metadata using the built-in napari console:img = viewer.layers[0].metadata["aicsimage"] img.dims.order # TCZYX img.channel_names # ["Bright", "Struct", "Nuc", "Memb"] img.get_image_dask_data("ZYX") # dask.array.ArrayThe napari layer metadata dictionary also stores a shorthand
for the raw image metadata:viewer.layers[0].metadata["raw_image_metadata"]The metadata is returned in whichever format is used by the underlying
file format reader, i.e. for CZI the raw metadata is returned as
anxml.etree.ElementTree.Element
, for OME-TIFF the raw metadata is returned
as anOME
object fromome-types
.Lastly, if the underlying file format reader has an OME metadata conversion function,
you may additionally see a key in the napari layer metadata dictionary
called"ome_types"
. For example, because the AICSImageIO
CZIReader
andBioformatsReader
both support converting raw image metadata
to OME metadata, you will see an"ome_types"
key that stores the metadata transformed
into the OME metadata model.viewer.layers[0].metadata["ome_types"] # OME object from ome-types
What's Changed
- bugfix/windows-tests-fix by @psobolewskiPhD in #41
- bugfix/windows-build-main-yml-matrix by @psobolewskiPhD in #42
- feature/store-access-to-aicsimage-and-raw-meta-in-layer-meta by @JacksonMaxfield in #43
- Update minimum
aicsimageio
version to v4.6.0: 40d8f8a - Update PyPI license to reflect the repo license: c18b6d0
New Contributors
- @psobolewskiPhD made their first contribution in #41
Full Changelog: v0.5.0...v0.6.0