The OMERO webclient framework allows raw data to be published to external web pages.
Selected datasets can be made visible to a ‘public user’ using the standard OMERO permissions system, ensuring you always have control over how users can interact with your data.
If you need another service for data publication, please visit the data management Home page.
¶ Public group creation and publishing data
Please email our OMERO team if you want to create a public group dedicated to your lab/unit.
¶ Share links to your published data
Log off from the private (regular) webclient (omero.epfl.ch), and then go to the public OMERO webclient omero-public.epfl.ch.
From this public page, browse in the public groups to select the item (image, dataset..) you want to share. You can create direct URLs to any item from a public group. To do so :
- Select the chosen element (image, dataset,...).
- Hit the
create link buttonin the right panel from the public OMERO webclient. - Paste this link and share it to people inside or outside EPFL ; they will be able to view your data without the need to enter credentials.
Here are a few examples of public URLs :
- to an image from a dataset : https://omero-public.epfl.ch/webclient/?show=image-2001
- to an image opened in the image viewer : https://omero-public.epfl.ch/webclient/img_detail/2001/?dataset=151
- to a dataset : https://omero-public.epfl.ch/webclient/?show=dataset-155
- to a project : https://omero-public.epfl.ch/webclient/?show=project-101
- to a tag : https://omero-public.epfl.ch/webclient/?show=tag-2452
¶ Guidelines to publish data with OMERO webclient
Please create separate projects for each individual publication, named "Author et al, date "
For each publication, we suggest you to create one dataset per figure / sub-figure
You can find the guidelines on OMERO under that project and dataset.
A full, real example is avialble on IDR
¶ Publication / project
Please provide us with the following information
- Study type
- Study description
- Publication title
- Publication authors
- Publication date (if it is already published)
- Publication DOI (if you already have it)
- Data Publisher
- Data DOI (if you have one)
- License
¶ Figure / dataset
Please provide us with the following information for each figure
- Figure legend
- Experiment type
- Organism + treatment
- Sample
- Imaging method
¶ Attachements and tags
- Attach the figures generated with OMERO.figure (PDF), and figures generated with other softwares to the raw images from which they were generated, and/or to the OMERO dataset that contains them.
- It is recommended to attach to datasets every files that describes the pipeline of how figures were generated from raw data. (text files, excels or .csv, processing scripts..).
- Data can also be tagged with OMERO tags to enhance the browsing possibilities through these data for any user with basic knowledge of OMERO. For example, tags can highlight the images displayed in the publication figures as images. Images only used for analysis which produced the published numerical data can also be tagged accordingly.
¶ Configuring URLs
The URL of the Project (corresponding to the publication) can be used for a DOI and data landing page. For example, https://omero.lifesci.dundee.ac.uk/webclient/?show=project-27936 corresponds to http://dx.doi.org/10.17867/10000109.
You can include this DOI directly in the publication, like in this example.
