{
"info": {
"author": "The Open Microscopy Team",
"author_email": "ome-devel@lists.openmicroscopy.org.uk",
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"Development Status :: 4 - Beta",
"Environment :: Plugins",
"Intended Audience :: Developers",
"Intended Audience :: End Users/Desktop",
"License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
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"description": ".. image:: https://travis-ci.org/ome/omero-metadata.svg?branch=master\n :target: https://travis-ci.org/ome/omero-metadata\n\n.. image:: https://badge.fury.io/py/omero-metadata.svg\n :target: https://badge.fury.io/py/omero-metadata\n\nOMERO metadata plugin\n=====================\n\nPlugin for use in the OMERO CLI. Provides tools for bulk\nmanagement of annotations on objects in OMERO.\n\nRequirements\n============\n\n* OMERO 5.4.0 or newer\n* Python 2.7\n\n\nInstalling from PyPI\n====================\n\nThis section assumes that an OMERO.py is already installed.\n\nInstall the command-line tool using `pip `_:\n\n::\n\n $ pip install -U omero-metadata\n\nNote the original version of this code is still available as deprecated code in\nversion 5.4.x of OMERO.py. When using the CLI metadata plugin, the\n`OMERO_DEV_PLUGINS` environment variable should not be set to prevent\nconflicts when importing the Python module.\n\nUsage\n=====\n\nThe plugin is called from the command-line using the `omero` command::\n\n $ bin/omero metadata \n\nHelp for each command can be shown using the ``-h`` flag.\nObjects can be specified as arguments in the format ``Class:ID``, such\nas ``Project:123``.\n\nBulk-annotations are HDF-based tables with the NSBULKANNOTATION\nnamespace, sometimes referred to as OMERO.tables.\n\nAvailable subcommands are:\n\n- ``allanns``: Provide a list of all annotations linked to the given object\n- ``bulkanns``: Provide a list of the NSBULKANNOTATION tables linked to the given object\n- ``mapanns``: Provide a list of all MapAnnotations linked to the given object\n- ``measures``: Provide a list of the NSMEASUREMENT tables linked to the given object\n- ``original``: Print the original metadata in ini format\n- ``pixelsize``: Set physical pixel size\n- ``populate``: Add metadata (bulk-annotations) to an object (see below)\n- ``rois``: Manage ROIs\n- ``summary``: Provide a general summary of available metadata\n- ``testtables``: Tests whether tables can be created and initialized\n\npopulate\n--------\n\nThis command creates an ``OMERO.table`` (bulk annotation) from a ``CSV`` file and links \nthe table as a ``File Annotation`` to a parent container such as Screen, Plate, Project\nor Dataset. It also attempts to convert Image or Well names from the ``CSV`` into\nImage or Well IDs in the ``OMERO.table``.\n\nThe ``CSV`` file can be provided as local file with ``--file path/to/file.csv``\nor as an OriginalFile in OMERO with ``--fileid 123``.\n\nIf you wish to ensure that ``number`` columns are created for numerical data, this will\nallow you to make numerical queries on the table.\nColumn Types are:\n\n- ``d``: ``DoubleColumn``, for floating point numbers\n- ``l``: ``LongColumn``, for integer numbers\n- ``s``: ``StringColumn``, for text\n- ``b``: ``BoolColumn``, for true/false\n- ``plate``, ``well``, ``image``, ``dataset``, ``roi`` to specify objects\n\nThese can be specified in the first row of a ``CSV`` with a ``# header`` tag (see examples below).\nThe ``# header`` row is optional. Default column type is ``String``.\n\nNB: Column names should not contain spaces if you want to be able to query\nby these columns.\n\nExamples:\n\nTo add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name``\nand ``Image Name``::\n\n $ bin/omero metadata populate Project:1 path/to/project.csv\n\nproject.csv::\n\n # header s,s,d,l,s\n Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name\n img-01.png,dataset01,0.0469,1,DAPI\n img-02.png,dataset01,0.142,2,GFP\n img-03.png,dataset01,0.093,3,TRITC\n img-04.png,dataset01,0.429,4,Cy5\n\nThis will create an OMERO.table linked to the Project like this:\n\n========== ============ ======== ============= ============ =====\nImage Name Dataset Name ROI_Area Channel_Index Channel_Name Image\n========== ============ ======== ============= ============ =====\nimg-01.png dataset01 0.0469 1 DAPI 36638\nimg-02.png dataset01 0.142 2 GFP 36639\nimg-03.png dataset01 0.093 3 TRITC 36640\nimg-04.png dataset01 0.429 4 Cy5 36641\n========== ============ ======== ============= ============ =====\n\nIf the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed.\n\nTo add a table to a Screen, the ``CSV`` file needs to specify ``Plate`` name and ``Well``.\nIf a ``# header`` is specified, column types must be ``well`` and ``plate``.\n\nscreen.csv::\n\n # header well,plate,s,d,l,d\n Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic\n A1,plate01,DMSO,10.1,10,25.4\n A2,plate01,DMSO,0.1,1000,2.54\n A3,plate01,DMSO,5.5,550,4\n B1,plate01,DrugX,12.3,50,44.43\n\nThis will create an OMERO.table linked to the Screen, with the\n``Well Name`` and ``Plate Name`` columns added and the ``Well`` and\n``Plate`` columns used for IDs:\n\n===== ====== ====== ============== =========== ================ =========== ===========\nWell Plate Drug Concentration Cell_Count Percent_Mitotic Well Name Plate Name\n===== ====== ====== ============== =========== ================ =========== ===========\n9154 3855 DMSO 10.1 10 25.4 a1 plate01\n9155 3855 DMSO 0.1 1000 2.54 a2 plate01\n9156 3855 DMSO 5.5 550 4.0 a3 plate01\n9157 3855 DrugX 12.3 50 44.43 b1 plate01\n===== ====== ====== ============== =========== ================ =========== ===========\n\nIf the target is a Plate instead of a Screen, the ``Plate`` column is not needed.\n\nLicense\n-------\n\nThis project, similar to many Open Microscopy Environment (OME) projects, is\nlicensed under the terms of the GNU General Public License (GPL) v2 or later.\n\nCopyright\n---------\n\n2018-2019, The Open Microscopy Environment",
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