10 Experimental Metadata Capture

This tool is designed to facilitate recording of experimental metadata, for annotation of images in OMERO.
OMERO.editor is an editing tool, where users can create a "template" (for example, to describe a protocol) and then use this template to create individual "experiment" files, which contain the experimental metadata. A summary of the experiment can be viewed alongside annotated images in OMERO.insight. This workflow makes it easy to reuse protocols, and to build up a detailed description of an experiment by combining several smaller protocols.
The OMERO.editor has been designed to achieve two key functions:

• Facilitate the digital recording of experimental metadata.
• Enable important parameters to be distinguished from the main text, e.g. to summarise the experiment in a concise form.

10.1 Launching OMERO.editor

There are two ways to launch OMERO.editor;

• As a standalone application by double clicking on the OMERO.editor icon found on your desktop
or


• Directly from OMERO.insight by clicking on the .

For the purpose of this tutorial we will work by launching the application from OMERO.insight.

Open OMERO.insight and click on the to open OMERO.editor.

Launching OMERO.editor will bring up the following main window:

This presents you with three options:

• Creating a new blank protocol
• Opening an existing protocol from the web
• Opening an existing protocol file

We will start by opening an existing protocol from the web and use this to give an general overview of the user interface by
clicking on the option. This will bring up the Import Demo File window as shown below:

To import a demo protocol we will select the 'Immunostaining protocol by clicking on the blue text, followed by pressing the import button.

• Open the Immunostaining web template protocol.

This will load the protocol in the editor, as shown below:

The workspace of the editor displays the complete protocol in the largest central panel. To the left, an outline of the protocol can be used for navigation and the panel on the right of the window is used for display and editing of parameter details.

The central panel can be used to view the protocol in a 'Text View' (below) or in a 'Tree View'

10.1.1 Text View

In order to make protocols appear more familiar to users, files can be viewed in a "Text" view, which displays the title, description and parameters in a page layout. This is the default protocol view.

10.1.2 Tree View

Protocols can also be viewed in the "Tree" view. You can switch between these views by using the tabs at the top of the page. The tree view gives you a better overview of the parameters and their hierarchical relationships. As shown below.

• Switch to tree view and expand the Stain node to reveal the antibody parameters.

10.2 Creating a new protocol.

We will now create a new protocol from scratch. To do so close any OMERO.editor sessions you have open and reopen OMERO.editor from OMERO.insight using the icon. This time we will choose the option.

• Open OMERO.editor from OMERO.insight and create a blank protocol.

This will bring up the following screen:

The first two 'steps' of the protocol has been added. This is the "Title Step" of the protocol, it's name can be edited in the top of the right panel. And the "Step 1" procedure.

• Give your new protocol a name such as: Immunostaining.

To add text to "Step 1", simply type in the step in the center panel. The step can also be given a name by editing in the right panel as before. In the example below, the text was copied, pasted and edited from a PDF protocol:

• Open OMERO.editor from OMERO.insight and create a blank protocol.

Enter some text into step 1 such as:

• Fix cells in methanol or paraformaldehyde.
• Permeabilize with 1% Triton X-100 in PBS for 15 minutes at room temperature.
• Block by incubating cells for 10 min in blocking buffer.
• Perform all blocking and antibody incubation steps in a humidified chamber.

We will now add another step to the protocol by using the icon. This will add a new step to our protocol where we can add further information as shown below:

Enter some text into step 2 such as:

• Incubate cells with primary antibodies diluted in blocking buffer for 35 mins to 1 hour.
• If you have never used the antibody before, try several dillutuins (low of 1:100 to high of 1:1000).
• Wash coversclips 3 x 10 minutes with PBS.
• Incubate coverslips for 15mins to 1hours with the appropriate secondary antibodies diluyted in blocking buffer, and wash 3 x 10 minutes with PBS

10.2.1 Creating Parameters

Now it's time to add parameters to this protocol. The "parameters" are variables in the protocol that change often and can be used to summarise the protocol. Parameters can be defined from existing text by highlighting the text, and clicking the "Add Parameter" icon beside the text.

• Highlight the methanol or paraformaldehyde text in step one and create a parameter by pressing and selecting Add drop-down menu parameter.

This will create a drop down box for this parameter. The drop down box can take a name and a list of values as shown below:

• Change the name to fixative and the dropdown contents to methanol, paraformaldehyde.

10.2.2 Managing steps

• Move step 2 to left of step 1 using the indent icon.
• Move step 1.1 to the right of step 1 using the indent icon.
• Move step 2 to be on top of step 1.
• Now delete this step.

10.2.3 Saving the protocol

The protocol can be saved using the icon. This will bring the options of saving to the server or to a local file, as shown below:

• Save your protocol to the server, you will be prompted for a file name.

Once you have saved your protocol on the OMERO server, you will be able to find the protocol under the Attachements panel in OMERO.insight as shown below: