OMERO & web

Presentation Outline

My background
OME Project
OMERO
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)

OME

Open Microscopy Environment

A typical microscopy
workflow

Interoperability

OMERO is a server with clients

OMERO API

Uses ICE (ZeroC) for remote API access

OMERO.web framework

OMERO.web documentation

webgateway API

Json data: e.g. Image json webgateway/imgData/<imageId>/

Image rendering: webgateway/render_image/<imageId>/<z>/<t>/

See WebGateway documentation

Show a Dataset of images


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


  <!-- dataset.html -->
  <html><body>

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

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

  </body></html>

See Creating an app documentation

App examples

Ship with OMERO.web:
- webgateway | webclient | webadmin
External sites:
- Stowers ODR | Sysgro (pombe) | JCB DataViewer
OME projects:
- OMERO.figure | OMERO.searcher | OMERO.webtagging
Examples & Prototypes:
- webtest | OMERO.gallery

OMERO.figure

http://will-moore.github.io/figure/

Services used by OMERO.figure

OMERO.figure tech

Backbone.js
- model
- events
- view
- templating
- router
Bootstrap - css, icons, js
Mousetrap - Keyboard bindings
Raphael - Drag handles etc
Reportlab - PDF generation

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

Adding web apps to OMERO

Comb Bio Seminar

8th December 2014

Will Moore

OMERO & web

Presentation Outline

My background

OME

Open Microscopy Environment

A typical microscopy
workflow

Interoperability

OMERO is a server with clients

OMERO API

OMERO.web framework

webgateway API

Show a Dataset of images

App examples

OMERO.figure

Services used by OMERO.figure

OMERO.figure tech

Future work

Thank you

Adding web apps to OMERO

Comb Bio Seminar

8th December 2014

Will Moore

OMERO & web

Presentation Outline

My background

OME

Open Microscopy Environment

A typical microscopyworkflow

Interoperability

OMERO is a server with clients

OMERO API

OMERO.web framework

webgateway API

Show a Dataset of images

App examples

OMERO.figure

Services used by OMERO.figure

OMERO.figure tech

Future work

Thank you

A typical microscopy
workflow