Open Microscopy Environment

In this example in IDR,

https://idr.openmicroscopy.org/webclien ... ge-1920105

the image has Attributes that hold information about Gene and Organism etc. I'd like to use this feature myself in our server as well, but could not find information. Is it related to OMERO.mapr?

How can I add Attributes to an image?

Hi Kouichi,

These Attributes are just MapAnnotations. First, we added configuration to change the standard "Key-Value Pairs" section to "Attributes":

Code: Select all

/opt/omero/web/OMERO.web/bin/omero config get | grep Attr
omero.web.ui.metadata_panes=[{"index": 0, "name": "map", "label": "Attributes"}, {"index": 1, "name": "table", "label": "Tables"}, {"index": 2, "name": "file", "label": "Attachments"}, {"index": 3, "name": "comment", "label": "Comments"}, {"index": 4, "name": "tag", "label": "Tags"}, {"index": 5, "name": "rating", "label": "Ratings"}, {"index": 6, "name": "other", "label": "Others"}]


Then, the specific information on Genes & Organisms does indeed come from OMERO.mapr:

Code: Select all

$ /opt/omero/web/OMERO.web/bin/omero config get | grep mapr
omero.web.apps=["django_prometheus", "omero_mapr"]
omero.web.mapr.config=[{"menu": "gene", "config": {"default": ["Gene Symbol"], "case_sensitive": true, "all": ["Gene Symbol", "Gene Identifier"], "ns": ["openmicroscopy.org/mapr/gene"], "label": "Gene"}}, {"menu": "genesupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/gene/supplementary"], "label": "Gene supplementary"}}, {"menu": "sirna", "config": {"default": ["siRNA Identifier"], "all": ["siRNA Identifier", "siRNA Pool Identifier"], "ns": ["openmicroscopy.org/mapr/sirna"], "label": "siRNA"}}, {"menu": "sirnasupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/sirna/supplementary"], "label": "siRNA supplementary"}}, {"menu": "phenotype", "config": {"case_sensitive": true, "all": ["Phenotype", "Phenotype Term Accession"], "default": ["Phenotype"], "label": "Phenotype", "wildcard": {"enabled": true}, "ns": ["openmicroscopy.org/mapr/phenotype"]}}, {"menu": "compound", "config": {"default": ["Compound Name"], "case_sensitive": true, "all": ["Compound Name"], "ns": ["openmicroscopy.org/mapr/compound"], "label": "Compound"}}, {"menu": "compoundsupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/compound/supplementary"], "label": "Compound supplementary"}}, {"menu": "organism", "config": {"default": ["Organism"], "all": ["Organism"], "ns": ["openmicroscopy.org/mapr/organism"], "wildcard": {"enabled": true}, "label": "Organism"}}, {"menu": "antibody", "config": {"default": ["Antibody Identifier"], "case_sensitive": true, "all": ["Antibody Identifier"], "ns": ["openmicroscopy.org/mapr/antibody"], "label": "Antibody"}}, {"menu": "antibodysupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/antibody/supplementary"], "label": "Antibody supplementary"}}, {"menu": "orf", "config": {"default": ["ORF Identifier"], "all": ["ORF Identifier"], "ns": ["openmicroscopy.org/mapr/orf"], "label": "ORF"}}, {"menu": "orfsupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/orf/supplementary"], "label": "ORF supplementary"}}, {"menu": "cellline", "config": {"default": ["Cell Line"], "all": ["Cell Line"], "ns": ["openmicroscopy.org/mapr/cell_line"], "wildcard": {"enabled": true}, "label": "Cell Lines"}}, {"menu": "celllinesupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/cell_line/supplementary"], "label": "Cell Lines supplementary"}}, {"menu": "others", "config": {"default": ["Others"], "all": ["Others"], "ns": ["openmicroscopy.org/omero/bulk_annotations"], "label": "Others"}}]
omero.web.public.url_filter=^/(webadmin/myphoto/|mapr/|webclient/(?!(action|annotate_(file|tags|comment|rating|map)|script_ui|ome_tiff|figure_script))|webgateway/(?!(archived_files|download_as)))
omero.web.ui.top_links=[["Studies", {"query_string": {"experimenter": -1}, "viewname": "webindex"}, {"title": "Image Data Repository"}], ["Genes", {"query_string": {"experimenter": -1}, "viewname": "maprindex_gene"}, {"title": "Genes browser"}], ["Phenotypes", {"query_string": {"experimenter": -1}, "viewname": "maprindex_phenotype"}, {"title": "Phenotypes browser"}], ["Cell Lines", {"query_string": {"experimenter": -1}, "viewname": "maprindex_cellline"}, {"title": "Cell Lines browser"}], ["siRNAs", {"query_string": {"experimenter": -1}, "viewname": "maprindex_sirna"}, {"title": "siRNAs browser"}], ["Antibodies", {"query_string": {"experimenter": -1}, "viewname": "maprindex_antibody"}, {"title": "Antibodies browser"}], ["Compounds", {"query_string": {"experimenter": -1}, "viewname": "maprindex_compound"}, {"title": "Compounds browser"}], ["Organisms", {"query_string": {"experimenter": -1}, "viewname": "maprindex_organism"}, {"title": "Organisms browser"}], ["About", "https://idr.openmicroscopy.org/about/", {"title": "About the Image Data Resource"}]]


You'll likely want to start with a much simpler configuration to test that everything is working. See for example https://github.com/ome/omero-mapr/#config-settings.

Cheers,
~Josh