OMERO'editor

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OMERO.editor
Stand-Alone
open microscopy environment

• A tool for scientists to record their
  experimental metadata.

William Moore Swedlow Lab, Dundee. will_at_lifesci.du
ndee.ac.uk
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Metadata everywhere!
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
Lab note-book
Word documents, Spreadsheets etc
Web sites http//lamondlab.com/f7immunostainprotoc
ol.htm
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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 1100 to high of
11000, for example). Wash coverslips 3 X 10
minute with PBS http//lamondlab.com/f7immunosta
inprotocol.htm
LAB NOTE-BOOK 10th May 08 Fixed cells in
PFA. Stained with Anti-Aurora-B (1250),
Anti-Tubulin (1500).
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A static form to record variables
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Users need to create and edit their own
forms/data structures
Edit protocol / data model
Edit Experimental variables
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A users collection of protocols
Jean-Francois Maure
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combined to create a digital lab note-book
Jean-Francois Maure
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XML import
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OME-XML
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Import of Ontology terms
http//www.ebi.ac.uk/ontology-lookup/
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Dates used to plan and archive

• Pick a date (date picker)
• Choose relative dates (eg 1 day later)
• Set alarm reminders
• Display dates in Calendar

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Browse old experiments
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Export to other calendars
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Keyword searching or More-Like-This search
http//lucene.apache.org/
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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.

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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/Omer
  oEditor