1. OMERO.editor A tool for scientists to record their experimental metadata. open microscopy environment William Moore Swedlow Lab, Dundee. will@lifesci.dundee.ac.uk “Stand-Alone”

2. Metadata everywhere! Lab note-book Fix and Stain Cells Prepare 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 etc Web sites http://lamondlab.com/f7immunostainprotocol.htm open microscopy environment

3. 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 cells Incubate 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-BOOK 10th May ‘08 Fixed cells in PFA. Stained with Anti-Aurora-B (1:250), Anti-Tubulin (1:500). open microscopy environment

4. A static form to record variables open microscopy environment

5. Users need to create and edit their own forms/data structures Edit “Experimental” variables Edit “protocol” / data model open microscopy environment

6. A user’s collection of protocols… open microscopy environment Jean-Francois Maure

7. … combined to create a “digital lab note-book” open microscopy environment Jean-Francois Maure

8. XML import open microscopy environment

9. OME-XML open microscopy environment

10. Import of Ontology terms http://www.ebi.ac.uk/ontology-lookup/ open microscopy environment

11. Dates used to plan and archive open microscopy environment Pick a date (date picker) Choose “relative” dates (eg 1 day later) Set alarm reminders Display dates in Calendar

12. Browse old experiments open microscopy environment

13. Export to other calendars open microscopy environment

14. Keyword searching or “More-Like-This” search open microscopy environment http://lucene.apache.org/

15. 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

16. 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 http://trac.openmicroscopy.org.uk/shoola/wiki/OmeroEditor open microscopy environment