Publishing data using OMERO.web
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Version 8 of 14: You are viewing an older version of this document, as it appeared on Jan 22 2021, 18:31.

Post-publication sharing of raw data

The OMERO.web 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.

To begin with

You need to be made a member of a public group on the EPFL OMERO server before you can start sharing data.

Public group creation

Please contact Claire Stoffel if you want to create a public group dedicated to your lab/unit.

Add data to a public group

You can either move data from an existing group into a public group, or import data directly into a public group

Move data from a private to a public group

To move data into a public group, select a project, dataset or an image in the left
hand pane (from the OMERO.insight client or from OMERO.web)
Right-click and select Move to Group ... in the menu, and choose the public group you belong to.

Add new data to a public group

To import data directly into a public group, go to File > Import... in the OMERO.insight client. In the Import Location window, choose the public group you belong to in the Group drop-down menu.

You always remain the owner of any of your images in a public group, and can still change rendering settings, add ROIs or annotate them.

Share links to your published data

You can create direct URLs to any element from a public group: To do so, select the chosen element (image, dataset,...) and hit the create link button in the right panel from OMERO.web. Paste this link and share it to people inside or outside EPFL, and 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.epfl.ch/webclient/?show=image-6093
to an image opened in the image viewer : https://omero.epfl.ch/webclient/img_detail/6082/?dataset=742
to a dataset : https://omero.epfl.ch/webclient/?show=dataset-743
to a project : https://omero.epfl.ch/webclient/?show=project-528
to a tag : https://omero.epfl.ch/webclient/?show=tag-11859

Guidelines to publish data with OMERO.web

Please contact Claire Stoffel if you want to create a public group dedicated to your lab/unit.

The created group will be named UNIT Public

Data layout:

Projects and Datasets

Please create separate projects for each individual publication, named "Author et al, date "

Under "Project details" (right panel), you can add useful general informations on your publication, like the complete name and the DOI.

Still at the project level, Key-Value pairs can be used to add more detailed informations on your publication:

You can create datasets for each figure or sub-figure of your publication

At the dataset level, under "Dataset details" (right panel), you can add the complete legend of the publication figure or sub-figure that correspond to your dataset

You can also make use of Key-Value pairs at the dataset level to add more detailed informations on each figure.

Import the raw images that were used to create each figure from the publication in the corresponding OMERO dataset.

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.