Metadata Handling

OME Users meeting
31th May 2018
Will Moore | Petr Walczysko | Jean-Marie Burel

Outline

• OMERO metadata: Annotations and OMERO.tables
• Map Annotations vs OMERO.tables
• OMERO.mapr: querying data by Map Annotations
• OMERO.parade: filtering data by metadata
• OMERO.figure: use metadata to create figures

Metadata in OMERO

• Image acquisition metadata
• Various Annotations
  • Tag
  • Comment
  • Long (rating)
  • File
  • Map
• OMERO.table (HDF table)

Map Annotation

• List of Key: Value in each Annotation
• Shown in right panel of clients
• Can be edited in right panel if namespace omero.constants.metadata.NSCLIENTMAPANNOTATION
• Suitable for unstructured / sparse data
• Each Annotation linked to 1 Image
• Can be queried with the QueryService

OMERO.tables

• HDF table saved as File in OMERO
• Typically 1 row per Image / Well
• Designed to "Write once, read often"
• Table linked to parent Screen/Plate/Project as File Annotation
• Can't be queried with the QueryService

OMERO.mapr for IDR

• OMERO.web app to query Images/Wells via Map Annotations
• E.g. "Give me all Screens that contain Images with Key Gene Symbol and Value CDC6"
• Config specifies which Annotation Namespaces and Keys are supported

# Example from IDR. Search for Genes.
$ bin/omero config append omero.web.mapr.config '{"menu": "gene", "config": {
    "default": ["Gene Symbol"],
    "all": ["Gene Symbol", "Gene Identifier"],
    "ns": ["openmicroscopy.org/mapr/gene"],
    "label": "Gene"}}'

# Namespace for User-added Map Annotations. "all" is empty for ANY key
$ bin/omero config append omero.web.mapr.config '{"menu": "keyvalue", "config": {
    "default": ["Any Value"],
    "all": [],
    "ns": ["openmicroscopy.org/omero/client/mapAnnotation"],
    "label": "KeyValue"}}'

OMERO.parade

• OMERO.web app to filter Images and Wells by their metadata
• By default, supports ROI counts, Rating, Tags, Map Annotations, Table Data
• Can be extended to use any metadata from OMERO
• Demo: OMERO.parade 0.1.0

$ pip install -U omero-parade

# Add parade custom app to your installed web apps:
$ bin/omero config append omero.web.apps '"omero_parade"'

# Display parade in the centre of the webclient:
$ bin/omero config append omero.web.ui.center_plugins \
    '["Parade", "omero_parade/init.js.html", "omero_parade"]'

OMERO.figure usage of Metadata

• Scalebars from pixel sizes
• Labels from:
  • Timestamps
  • Channel names
  • Dataset name
  • Tags
• ROIs - Polygons and Polylines supported in 4.0.0 (May 2018)