Add support for OME-NGFF ZARR inputs #45
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
zivy
reviewed
Jun 8, 2023
README.rst
Outdated
| @@ -52,7 +52,8 @@ Sample data is available and described on Zenodo: | |||
| :target: https://doi.org/10.5281/zenodo.4304786 | |||
|
|
|||
| Any image and transform file format supported by `SimpleITK's IO <https://simpleitk.readthedocs.io/en/master/IO.html>`_ | |||
| can be use by sitk-ibex. The 3D `nrrd` format, and `txt` transform file extension are recommended. | |||
| can be use by sitk-ibex. The NRRD or`NGFF <https://ngff.openmicroscopy.org/latest/>`_ image format, and `txt` transform file | |||
README.rst
Outdated
| .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4632320.svg | ||
| :target: https://doi.org/10.5281/zenodo.4632320 | ||
|
|
||
| The sample Imaris files can be converted to OMG-NGFF ZARR with |
README.rst
Outdated
|
|
||
| These images will be registered based on the common "Hoechst". The name of the channels are lost in this conversion from | ||
| Imaris to OME-NGFF ZARR. Some conversions produce "omera" metadata in the ZARR file which contains channel labels, which | ||
| can be used. When then channel label are unavailable, the channel index can be used such as the following commands:: |
| if isinstance(channel, int): | ||
| channel_number = channel | ||
| else: | ||
| if "omero" not in zarr_group.attrs or "channels" not in zarr_group.attrs["omero"]: |
There was a problem hiding this comment.
Is the existence of "omero" specific to the converter used to create the OME-Zarr files? Not sure what the relationship is between OMERO (microscopy image storage/management system) and the OME-Zarr format.
There was a problem hiding this comment.
The ngff meta-data is documented here: https://ngff.openmicroscopy.org/latest/index.html#omero-md. The "omero" field is optional and "transitional".
OME stands for "Open Microscopy Environment". OMERO is from the same group.
zivy
approved these changes
Jun 8, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.