Metadata-Version: 1.2
Name: omero-cli-zarr
Version: 0.0.10
Summary: Plugin for exporting images in zarr format.
Home-page: https://github.com/ome/omero-cli-zarr/
Author: The Open Microscopy Team
Author-email: 
License: UNKNOWN
Description: .. image:: https://github.com/ome/omero-cli-zarr/workflows/Precommit/badge.svg
           :target: https://github.com/ome/omero-cli-zarr/actions
        
        .. image:: https://badge.fury.io/py/omero-cli-zarr.svg
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        OMERO CLI Zarr plugin
        =====================
        
        This OMERO command-line plugin allows you to export Images and Plates
        from OMERO as zarr files, according to the spec at
        https://github.com/ome/omero-ms-zarr/blob/master/spec.md
        as well as Masks associated with Images.
        
        Images are 5D arrays of shape `(t, c, z, y, x)`.
        Plates are a hierarchy of `plate/row/column/field(image)`.
        Masks are 2D bitmasks which can exist on muliplte planes of an Image.
        In `ome-zarr` sets of Masks are collected together into "labels".
        
        It supports export using 2 alternative methods:
        
        - By default the OMERO API is used to load planes as numpy arrays
          and the zarr file is created from this data. NB: currently, large
          tiled images are not supported by this method.
        
        - Alternatively, if you can read directly from the OMERO binary
          repository and have installed https://github.com/glencoesoftware/bioformats2raw
          then you can use this to create zarr files.
        
        
        Usage
        -------
        
        Images and Plates
        ^^^^^^^^^^^^^^^^^
        
        To export Images or Plates via the OMERO API::
        
        
            # Image will be saved in current directory as 1.zarr
            $ omero zarr export Image:1
        
            # Plate will be saved in current directory as 2.zarr
            $ omero zarr export Plate:2
        
            # Specify an output directory
            $ omero zarr --output /home/user/zarr_files export Image:1
        
            # Cache each plane as a numpy file.npy. If connection is lost, and you need
            # to export again, we can use these instead of downloading again
            # omero zarr --cache_numpy export Image:1
        
        
        To export images via bioformats2raw we use the ```--bf``` flag::
        
            export MANAGED_REPO=/var/omero/data/ManagedRepository
            export BF2RAW=/opt/tools/bioformats2raw-0.2.0-SNAPSHOT
        
            $ omero zarr --output /home/user/zarr_files export 1 --bf
            Image exported to /home/user/zarr_files/2chZT.lsm
        
        Masks
        ^^^^^
        
        To export Masks for an Image or Plate::
        
            # Saved under 1.zarr/labels/0 - 1.zarr/ must already exist
            $ omero zarr masks Image:1
        
            # Labels saved under each image. e.g 2.zarr/A/1/0/labels/0
            # Plate should already be exported
            $ omero zarr masks Plate:2
        
            # Saved under zarr_files/1.zarr/labels/0
            $ omero zarr --output /home/user/zarr_files masks Image:1
        
            # Specify the label-name. (default is '0')
            # e.g. Export to 1.zarr/labels/A
            $ omero zarr masks Image:1 --label-name=A
        
        The default behaviour is to export all masks on the Image to a single 5D
        "labeled" zarr array, with a different value for each mask Shape.
        An exception will be thrown if any of the masks overlap.
        
        To handle overlapping masks, split masks into non-overlapping zarr groups
        using a "label-map" which is a csv file of that specifies the name of
        the zarr group for each ROI on the Image. Columns are ID, NAME, ROI_ID.
        
        For example, to create a group from the `textValue` of each Shape,
        you can use this command::
        
            omero hql --style=plain "select distinct s.textValue, s.roi.id from Shape s where s.roi.image.id = 5514375" --limit=-1 | tee 5514375.rois
        
        This creates a file `5514375.rois` like this::
        
            0,Cell,1369132
            1,Cell,1369134
            2,Cell,1369136
            ...
            40,Chromosomes,1369131
            41,Chromosomes,1369133
            42,Chromosomes,1369135
            ...
        
        This will create zarr groups of `Cell` and `Chromosomes` under `5514375.zarr/labels/`::
        
            $ omero zarr masks Image:5514375 --label-map=5514375.rois
        
Keywords: OMERO.CLI,plugin
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Plugins
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Information Technology
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3
