5 Remote Web Access

The OMERO.web client is a web based client that provides remote access to OMERO using the standard web browser.

5.1 Logging In

To log in OMERO.web open the firefox web browser by clicking the icon found on the desktop.
The OMERO web address will be made available for you to enter into the address bar:

This will bring up the OMERO.web log in screen as shown below.

We shall provide you with the OMERO login details. Fill in the username and password details in the appropriate sections. Once you have filled in your account details proceed to click on the CONNECT button.

5.2 The Home Page

Upon login the home page will appear as shown below:

The home page contains on the left hand side you most recently imported image and on the right hand side your most recent tags, comments and shares. This provides quick access to any recent data. At the top is a toolbar that looks like this:

The toolbar allows you to navigate to the different pages of the web client.

Exercise 1:

• Use the toolbar to navigate to the Data page.

5.3 The Data Page

The data page replicates some of the functionality found in OMERO.insight. The default view in the data page is the by now familiar hierarchies.

5.3.1 Hierarchies

The hierarchies presents the user with the projects/datasets/images tree view of the data as shown below.

Users can expand the tree using the icon.

Exercise 2:

• Expand the hierarchy to locate one of your images.

The data is presented in a similar manner to OMERO.insight, with the hierarchy on the left hand side, the workspace in the center, and the metadata browser and preview viewer on the right.

Exercise 3:

• Select one of your images in the hierarchy view.
• Use the preview panel to browse the Z axis of you image
• Click on the metadata tab to locate your images microscope details

5.3.1.1 Managing the hierarchy

The hierachy can also be managed from the web client. It is possible to create new Projects and Datasets and Screens using the icons. You will only be able to create a Dataset when you have selected a Project. To create a Project, first select the User at the top of the hierarchy. You can manage the hierarchy with the copy, paste, cut and delete operators using the icons. These functions can also be found using a right-click menu on the tree.

Exercise 4:

• Try creating a new project and attaching an existing dataset to this project.

5.3.2 Tags

An alternative view to the projects/datasets/images hierarchy is the tag view. You can switch from the hierarchy view to the tag view by clicking on the icon. This will present you with the tag view as shown below:

To switch back to the hierarchy view click on the icon.

Exercise 5:

• Try switching between the hierarchy view and the tag view.

In the tag view, view your tags. To see the images belonging to a particular tag click on the icon.

5.3.3 Data Viewer

OMERO.web also has a data viewer providing more control over data visualisation. To access the data viewer select an image and click on the icon. You can also double-click on thumbnails or images in the hierarchy. This will bring up the following new window.

Exercise 6:

• Select an image
• Open the data viewer for the selected image.
• Using the data viewer it is possible to access many of the features present in the OMERO.insight data viewer. The viewing options can be toggled from between normal, maximum intensity projection and split channel views. It also possible to toggle each channel independently. Sliders allow for both exploration of the Z and T axis.
• The Channels: Edit link allows you to adjust and save rendering settings for each channel.

Exercise 7:

• Switch between the three different viewing options.
• Toggle channels on and off.
• Explore the Z and T dimensions of your image.

One of the most useful feature of the data viewer is the ability to share the current view with another user using the Image Link. The image link will provide you with a URL that you can use to share with other users or embed on other web pages.

5.3.4 Sharing your Data

One of the most important features of the OMERO.web client is the ability to share data between users. Images can be shared by adding them to the basket. When an image is selected press the icon to add it to the basket. You will notice that the basket status will be updated to reflect contents being added to it. This is shown at the top of the page like this:

Exercise 8:

• Select an image and add it to the basket
• Repeat this for another image so that your basket contains 2 items

To view the basket contents click on the BASKET link, this will bring up the following screen:

This displays the items in your basket. Items can be selected by clicking on them. You can remove items by clicking on the icon. The basket contents can be completely emptied using the icon.

Exercise 9:

• Empty the contents of the basket

To share images two options are available. It is possible to setup a discussion using the icon or a share using the . When setting up a share or discussion you will be asked to enter an initial message, select an expiration date if required and select the users to share with.

Exercise 10:

• Select an image and add it to your basket
• Create a share for the image with a the person sitting next to you, you will require to know their user name
• Create a discussion with the people sitting around you

5.4 The Public Page

The public page contains the items you have shared with other members in your group. This page can be accessed using the Public icon found in the top toolbar.

You can expand the items in the public page to reveal the images in a share. The discussion items will contain a history of the conversation in the Annotation section.

Exercise 11:

• Locate an image share
• Locate a discussion share and view the conversation by clicking on the Annotation.

5.5 The Search Page

The search page can be accessed by clicking on the search icon in the toolbar. This will bring up the screen found below.

You can search for images in the same way you did in OMERO.insight.

Exercise 12:

• Search for all images ending with the word 'ing'.

5.6 The History Page

The history page can be accessed by clicking on the history icon on the toolbar. This will bring up the following screen.

The history page presents you with a calendar view of your imported data. You can use the calender to browse your images based on the date they were imported.

Exercise 13:

• Locate an image you imported today by exploring today's date.

5.7 The Me Page

The me page can be accessed by clicking on the me icon in the toolbar. This will bring up the following page:

The me page allows you to access and edit your profile settings.

5.8 The Help Page

The help page is accessed by clicking on the help icon in the toolbar.

The help page is a link to the OMERO features page where movies and web pages can be accessed to illustrate specific features of OMERO.

5.9 The Contact Page

The contact page, accessed using the contact icon on the toolbar, allows you to send feedback to the OMERO developer team.