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3 Managing Your Data

To manage your data the OMERO.insight application is a user friendly client created to facilitate the management, viewing and analysis of data on the OMERO system.

3.1 The Default View

The OMERO.insight default view is made up of three sections: (1), (2) and (3).

  • Section (1) is the inspector panel.
  • Section (2) is the working area panel.
  • Section (3) is the metadata browser panel.

3.2 The Inspector Panel - Hierarchies

3.2.1 Navigating the Hierarchies

We will start by navigating the hierarchy to locate some of the data that we imported earlier. One view of our images on the OMERO server is using the Project, Dataset, Image hierarchy.
Click on one of the icons in the Hierarchy section of the inspector panel. This will expand the selected Project to reveal the Datasets belonging to this Project. In a similar manner expand a Dataset to reveal if any images are contained within the selected Dataset. This is the basic Project / Dataset / Image hierarchy. Repeat this process until an image is selected, as illustrated below:


We now have an image called Substack (51-101)TOP.tif that belongs to the Dataset Single Channel that belongs to the Project called Confocal Data.

Exercise 1

  • Explore the hierarchy of the various projects/datasets/images you created and imported earlier.

3.2.2 Managing the Hierarchies

In OMERO.insight it is possible to manage the hierarchies. You can create new projects/datasets and attach images to one or more of these hierarchies. To create a new Project click on the icon. This will bring up the menu shown below.


Using this menu you select the New Project menu item. The following window will then appear.


You will need to set a name for your new Project. Then press the Create button. A new Project will be created in the OMERO server, and displayed in the inspector.
To add a new Dataset to a Project,

  • Select a Project
  • Right-click on the selected Project.
  • Then select New Dataset... from the pop-up menu.
    • Or
  • Click on the icon.
  • And select New Dataset
  • Then the Create dialogue will pop up.

Once created, the new Dataset will appear under the selected Project. Renaming of Projects, Datasets and Images is described below.

Exercise 2
  • Try creating more than one dataset in a project.

3.2.3 Cut / Copy / Paste / Delete

Four basic operations are possible on the hierarchy using the inspector panel.

Cut: (i.e. unlink) A dataset/image from its parent.
Copy: Copy a dataset/image to then be able to paste it to a parent object.
Paste: (i.e. link) Paste a dataset/image to its parent.
Delete: Delete a project/dataset/image from the server.

These operators can be accessed by either:

Pressing the icon found at the top of the inspector panel. and/or Right clicking on a selected Project/Dataset/Image. and/or Pressing on the Edit menu bar entry.

When deleting a Project or Dataset, you will have the choice of whether to delete it's contents. If you decide not to, the contents will become orphaned. Orphaned Datasets will appear in the hierarchy tree. All images (including orphans) can be found under the 'Images' tab below the hierarchy tab.

Exercise 3
  • Cut a Dataset from one Project and paste it in a different Project.
  • Copy an Image from a Dataset to another Dataset.
  • Find or create an empty Dataset and delete it.

3.3 The Working Area Panel

The working area panel allows you to view the Images belonging to a Dataset or Project. Try to select a dataset that contains some Images as illustrated below:

You will notice that Section (2) ,the working area panel, contains thumbnails of your images that belong to this Dataset. It is also possible to select a Project and press the icon found on the top icon bar as shown below:

This will generate a view of all the images grouped in the datasets belonging to the project as shown below:

Exercise 4
  • Try generating a thumbnail view for a Project.

3.3.1 The Working Area Toolbar.

The Working Area has a toolbar to control various options found on the top of the panel, as shown below.

Using this toolbar it is possible switch between a list view or a thumbnail view of your images by toggling the icons.

The view can be refreshed using the icon.

The images can be either ordered by Name or by Acquisition date by toggling the icons.

A mouse over zoomed view of images can be toggled using the icon.

The number of images per row for the thumbnail view can also be overridden and set manually using the input field.

Exercise 5
  • Try switching from thumbnail view to list view.
  • Order your images by acquisition date.
  • Switch to the thumbnail view and set 2 images per row.

The remaining options of the top toolbar are covered in later sections. At the bottom of the working area there is also the following toolbar to allow you to control the thumbnail sizes.

This allows you to either increase/decrease the thumbnail size in small steps by using the icons. Reset the size to it's default using the icon. Specify the thumbnail size using the zoom slider.

Exercise 6
  • Try changing the image thumbnail size by using the zoom slider.
  • Reset the thumbnail size to default.

3.4 The Metadata Browser Panel

OMERO allows for various types of metadata to be associated with an Image. This can be:

  • Image and Acquisition metadata from the original file
  • Attachements (PDF, Word, Excel, etc.)
  • Ratings
  • Comments
  • Tags

This information is a made available in the metadata browser panel.

3.4.1 Image and Acquisition metadata

Select an image in the workspace panel. In Section (3), the metadata browser panel, information about your image will then appear as shown below:

The General tab will contain information about your image such as the

  • Name
  • Description
  • Image dimensions, X,Y,Z,C,T
  • Pixel Size in microns

    • Note that it is possible to edit some of these fields using the icon. The Name and Description field are also available to Projects and Datasets. When you have edited these fields, you can save the change using the 'Save' icon in the tool bar at the top of the metadata pane.

    Exercise 7

    • Change the name of your image.
    • Add some text to the image description.
    • Rename a Project

    At the time of import OMERO will also try to capture metadata about the image acquisition contained in the original file. This can be viewed by selecting the Acquisition tab as shown below.

    This will contain acquisition information such as

    • Microscope
    • Channels
    • Exposure Times

    You can expand any of the sections using the icon and collapse them using the icon.

    Exercise 8
    • Check what type of laser was used to capture your image.
    • Expand the original metadata section to view all the metadata from the original file format

    3.4.2 Annotations

    Annotations can be added to an Projects, Datasets and Images. These can be:

    • Ratings
    • Comments
    • Attachments (PDF, Word, Excel, etc.)
    • Tags

    The annotations are found in the General tab of Section (3), the metadata browser panel.

    3.4.2.1 Ratings

    Ratings can be set, by using a 5 star rating system. A rating can be removed by pressing the icon. Changes to rating should be saved with the 'Save' icon in the tool bar.

    Exercise 9
    • Add a rating to an image

    3.4.2.2 Comments

    Comments are textual annotations. They also need to be saved using the tool bar 'Save' button.

    Exercise 10
    • Add a comment to an image

    3.4.2.3 Attachments

    To add an attachment use the icon and select a file on your local machine to attach. Attachments can be downloaded, viewed, and deleted by clicking the double arrow as shown below:

    Note that unlinking an attachment will remove the link, but will NOT delete the attachment from the server. It is also possible to unlink all attachments using the [-] icon.

    Exercise 11
    • Add an attachment to an image
    • Delete an attachment
    • Unlink an attachment
    • Download an attachment

    3.4.2.4 Tags

    Tags are keyword annotations that can be associated with Projects, Dataset and Images. To add a tag click on the icon. This will bring up the tag selection window shown below.

    Using the tag selection window a user can add and remove tags. New tags can also be created using the New tag field. To apply the tags press the Accept button. Tags can also be individually removed using the [-] icon in the metadata browser panel.

    Exercise 12
    • Try adding a few tags to an image.
    • Try removing a tag.

    3.5 The Inspector Panel - Screens

    In Section (1), the inspector panel, locate the Screens tab and expand it using the icon. You will be presented with the following:

    This will bring you a tree view to browse high content screening data in a hierarchy of screens and wells. Double clicking on the image will present the grid view of the wells, where individual images for the wells can be accessed.

    Exercise 13
    • Locate and expand a screen to view the individual wells.

    3.6 The Inspector Panel - Attachments

    In Section (1), the inspector panel, locate the Attachments tab and expand it using the icon. You will be presented with the following:

    This view allows you to browse all attachments present on the OMERO system.
    Click on the icon for Other Files and select one of the files you previously attached.
    In Section (3), the metadata browser panel, you will notice a section called Attached to. You can expand this section using the icon to retrieve information about what objects this file is attached too. Note it is also possible to delete file attachments from this view using the icon.

    Exercise 14
    • Locate and delete one of your file attachments using the attachments inspector panel.

    3.7 The Inspector Panel - Tags

    In Section (1), the inspector panel, locate the Tags tab and expand it using the icon. You will be presented with the following:

    A tag can belong to a parent object called a tag set. For example a typical arrangement could be:

    • Biological Processes
    • Cell Division
    • Cell Polarity
    • Differentiation
    • Growth
    • Patterning

    Where Biological Processes is the tag set and Cell Division, Cell Polarity, Differentiation, Growth, Patterning are the tags. Tag sets and tags can created by using the icon, you will then be presented with the choice of creating either a tag set or tag as shown below.You can also add a tag to a tag set by right-clicking on the tag set.

    Tags can be associated to tag sets using the cut, copy, paste operators.

    Exercise 15
    • Find the image you tagged earlier
    • Try creating a new tag set and adding tags to the tagset

    3.8 The Inspector Panel - Images

    In Section (1), the inspector panel, locate the Images tab and expand it using the icon. You will be presented with the following:

    This panel keeps a history of your imported images. It is possible to retrieve images based on the date that they where imported in the OMERO system.

    Exercise 16
    • Locate an image you imported today in the OMERO system

    3.9 The Inspector Panel - Search

    In Section (1), the inspector panel, locate the Search tab and expand it using the icon. You will be presented with the following:

    This panel allows you to search for images on the OMERO system. The search field allows you to enter textual terms to search for. It supports the following special characters:

    • * : Multiple characters wild card search.
    • ? : single character wild card search.
    • ^ : Boosting of terms.

    Results from the search will appear in Section (2), the workspace panel.

    3.9.1 Context

    Searches can be applied to multiple fields of an image. These can be included in the search by checking the check box of the items in the Context panel.

    Exercise 17
    • Find all images ending in 'ing'
    • Find all images that have an e as their second character in the name field.

    3.9.2 Advanced Searching

    Under the search field press the icon to reveal the advanced search options. You will then be presented with the following screen:

    This allows you more control over your search criteria. To go back to the basic search option press the "left arrow" icon.

    Exercise 18
    • Search for all images that start with the letter C and do not contain the word red

    3.9.3 Searching within a particular tag set / tag

    By pressing the icon, it is also possible to limit the search to a subset of tag sets and tags.

    Exercise 19
    • Search for all images in the tag set Arabidopsis whose description contains the word leaf

    3.10 Filtering Images in the Working Area

    Return to the hierarchies view by expanding it using the icon and select a dataset that contains some images. Using the working area toolbar at the top of the working area it is possible to filter images in the workspace by using the drop down box. To see the filter options click on the icon next to the filter images text. This will bring up the following list to allow for simple filtering.

    Exercise 20
    • Try filtering images by a specific name

    Note that the filter can be removed by selecting the Show all images option. It is also possible to filter images using a combination of these criteria by clicking on the icon. This will bring up the following dialogue box:

    A combination of criteria can be selected to perform more complex filters.

    Exercise 21
    • Try filtering images by the rating and date of acquisition.
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