omero.editor a tool for scientists to record their experimental metadata. open microscopy...
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OMERO.editorOMERO.editor
A tool for scientists to record their experimental metadata.
open microscopy environment
William Moore
Swedlow Lab, Dundee.
“Stand-Alone”
Metadata everywhere!
Lab note-book
Fix and Stain CellsPrepare formaldehyde by dissolving 1.85g powder in 10mls PBS.Warm in fume cupboard till solution is clear. Filter through 0.2uM filter. This is 37% solution…
Word documents,Spreadsheets etcWeb sites
http://lamondlab.com/f7immunostainprotocol.htm
open microscopy environment
Typical workflow…
Immunostaining:
Fix cells Fix cells in 3.7% Formaldehyde in PBS for 2 x 5 mins. Aspirate off fixative.Permeabilize with 1% Triton X-100 in PBS for 15 minutes at room temperature. Block by incubating cells for 10 min in blocking buffer (see below). We perform all blocking and antibody incubation steps in a humidified chamber.
Stain cellsIncubate cells with primary antibodies diluted in blocking buffer for 35mins to 1 hour. If you have never used the antibody before, try several dilutions (low of 1:100 to high of 1:1000, for example). Wash coverslips 3 X 10 minute with PBS…
http://lamondlab.com/f7immunostainprotocol.htm
LAB NOTE-BOOK10th May ‘08Fixed cells in PFA.Stained with Anti-Aurora-B (1:250), Anti-Tubulin (1:500).
open microscopy environment
A static form to record variablesopen microscopy environment
Users need to create and edit their own forms/data structures
Edit “Experimental” variablesEdit “protocol” / data model
open microscopy environment
A user’s collection of protocols…open microscopy environment
Jean-Francois Maure
… combined to create a “digital lab note-book”open microscopy environment
Jean-Francois Maure
XML importopen microscopy environment
OME-XMLopen microscopy environment
Import of Ontology terms
http://www.ebi.ac.uk/ontology-lookup/
open microscopy environment
Dates used to plan and archiveopen microscopy environment
• Pick a date (date picker)• Choose “relative” dates (eg 1 day later) • Set alarm reminders• Display dates in Calendar
Browse old experimentsopen microscopy environment
Export to other calendarsopen microscopy environment
Keyword searchingor “More-Like-This” search
open microscopy environment
http://lucene.apache.org/
Future: Integration with OMERO server and insight
• Upload OMERO.editor files to server.• Annotate Projects, Datasets, Images with
OMERO.editor files.• Index OMERO.editor files on server for
searching.• Display and edit OMERO.editor files from
within OMERO.insight.• View Date-Time fields in web-client calendar.
open microscopy environment
Summary
• OMERO.editor allows metadata to be modeled in a hierarchical structure.
• A “protocol” or “data model” can be edited separately from the experimental variables.
• This facilitates re-use of metadata models, while allowing for necessary flexibility.
• More info, demo movie & download: http://trac.openmicroscopy.org.uk/shoola/wiki/OmeroEditor
open microscopy environment