OMERO.editor Beta-4

The Beta-4 OMERO.editor is an 'Agent' of the OMERO.insight client, allowing it to connect to the OMERO server. It can also edit and save local files in the same way as the Beta-3 Editor. This has some implications for running Editor:

Start Editor via Insight

You can run the OMERO.editor as a standalone application (no server connection) OR via OMERO.insight. In Insight, you start Editor by clicking the Editor icon in the toolbar. In Insight, you can open any Editor file by double clicking it, either when you find it attached to a Project, Dataset or Image, or by browsing under View > Attachments (see screen shot).

Editing and UI Changes

A number of changes have been made to the editing of files in the Beta-4 OMERO.editor. The Beta-4 Editor will be able to open Beta-3 Editor ("pro.xml") files, although a number of features are not currently supported. See Protocol Model in Beta-4.

UI Layout

The Editor displays a single file per window, which will typically be split into 3 panels. The left of the UI displays a hierarchical outline of the file that can be used for navigating large files. The center is the main display of the file for editing experimental variables and the right panel is for editing the protocol 'template'.

Text View of protocols

In order to make protocols appear more familiar to users, files can now be viewed in a "Text" view, which displays the title, description and parameters in a page layout (below Left). Protocols can also be viewed in the "Tree" view, which resembles the Beta-3.0 Editor layout (below Right). You can switch between these views by using the tabs at the top of the page.

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Click images to see full-sized screen shots.

Multiple 'parameters' per step

In order to record a single step of a protocol that has multiple variables, E.g. "Incubate cells with {Antibody} at a dilution of {1:500} for {60 minutes}", OMERO.editor now supports multiple parameters per step (see screenshots below). Placing parameters in context with descriptions also allows a more natural way of combining multiple parameters and removes the need to give every parameter a description.

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Screen-shots of multiple parameters in the Text view (left) and the Tree view (right). In both cases, parameters can be seen in the context of the step description, which can be edited in the right panel of the Tree view, or the page layout of the Text view. Parameters can be edited in the right panel of both views.

Table of parameter values

For some steps in a protocol, the parameters can have more than one value. E.g. In the above example, several antibodies may be used for staining different targets, and each one will have a different concentration and staining time. OMERO.editor supports the documenting of this data by allowing the values for each parameter to be displayed in a table (add table with the icon in the Tree view). Each parameter is represented by a column, with the column name displaying the name of each parameter. 'Drop-down' and 'Check-box' parameters are represented with the appropriate controls in the table (see below).