Adding web apps to OMERO

Comb Bio Seminar

8th December 2014

Will Moore

OMERO & web

Presentation Outline

  • My background
  • OME Project
  • OMERO.web framework
  • App example: OMERO.figure

My background

  • Biochemistry at Bath Uni
  • PhD with Paul Clarke, Ninewells, Dundee
  • Postdoc with Jason Swedlow
  • MSc in Applied Computing
  • Joined OME team in 2007
    • OMERO.editor (Java)
    • OMERO.scripts (Python)
    • OMERO.web (Python, JS etc)


Open Microscopy Environment

A typical microscopy


OMERO is a server with clients


OMERO.web framework

OMERO.web documentation

webgateway API

See WebGateway documentation

Show a Dataset of images

  url( r'^dataset/(?P<datasetId>[0-9]+)/$', views.dataset ),
  def dataset(request, datasetId, conn=None, **kwargs):
    ds = conn.getObject("Dataset", datasetId)
    return render_to_response('dataset.html', {'dataset': ds})

  <!-- dataset.html -->

    <h1>{{ dataset.getName }}</h1>

    {% for i in dataset.listChildren %}
      <img src="{% url 'webgateway.views.render_thumbnail' %}" />
      {{ i.getName }}
    {% endfor %}

See Creating an app documentation

App examples


Services used by OMERO.figure

OMERO.figure tech

Future work

  • New OMERO.figure features
    • ROI support
    • Free form Labels
    • and lots more...
  • Improve webgateway coverage
    • Web apps are increasingly using json services
    • Need more complete json API
    • json services can be used by other clients

Thank you

  • Jason Swedlow
  • OME team