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4 Viewing Your Data

The OMERO.insight client has a built in viewer to view multi-dimensional images. To start we will select an image from either the inspector panel, hierarchies tab or directly from the workspace panel as shown below.

4.1 Image Preview

Notice how in the metadata browser panel there is a tab called Preview. Clicking on this tab will bring up the Image Preview panel as shown below.

The image preview panel provides a mini preview window of your image and allows you to tune some of the render settings without having to launch the full image viewer.
There are sliders to navigate through the Z and T dimensions of your images, as well as buttons to toggle channels on and off. The rendering of the image can be adjusted by changing the min/max threshold values for each channel.

Exercise 1
  • Navigate through the Z sections of your image.
  • Turn a channel on and off
  • Increase the minimum threshold value for a channel

4.2 Image Viewer

The image viewer includes more functionality to explore your images. To launch the image viewer, double click on an image in the workspace panel. This will bring up the image viewer window shown below:

Note that it is possible to have more than one image viewer open at once. To open multiple viewers simply double click on a different image in the workspace panel.

Exercise 2
  • Open two instances of the image viewer

4.2.1 Viewing Modes

There are three main viewing modes to examine an image. These are selected using the three tabs found on the top of the viewer. The default view is the image mode.

4.2.1.1 Image mode

In image mode the viewer has two sliders that can be used to navigate the Z and T dimensions of an image. To navigate the Z dimension in single increments the and icons can be used. The can be moved anywhere along the slider to move in larger increments.
The T dimension can be navigated in a similar manner.

Exercise 3
  • Explore the Z and T sections by moving the sliders.

The Z and T dimensions can also be animated by using the icon found next to the respective slider.


Exercise 4
  • Animate the Z dimension.

On the left hand side of the image viewer are various tools to control the image.

The icon allows you to toggle between colour or a greyscale rendering of your image.

The icon allows you to set the colours for each of your data channels.

The icons allow you to toggle the individual channels on or off.

The icon allows you to animate the channel toggling.

Exercise 5
  • Change the colour for one of your channels.
  • Toggle one of the channels on and off manually.
  • Animate the channel toggling.

The image can also be enlarged and reduced using the tool.

4.2.1.2 Split mode

By clicking on the Split tab in the image viewer, the split viewer is revealed as shown below.

This viewer presents the different channels of the image side by side. This is useful to allow direct comparison of channels whilst navigating the Z and T sections.

The allows you to toggle the channels from colour to greyscale.

The icons allow you to toggle the individual channels on or off.

The icon allows you to toggle the text labels for each view.

The images can also be enlarged and reduced using the tool.

Exercise 6
  • Produce a split view without labels and the channels in greyscale mode.

4.2.1.3 Projection mode

By clicking on the Projection tab in the image viewer, the projection viewer is revealed as shown below.



The projection viewer allows you to produce projections of your section images. The top part of the projection menu controls the what and how of the projection.

You can select a mean or maximum intensity projection.
You can also specify the sub-sampling of the Z dimension.
You can specify the range of Z-sections projected using the Z-sliders to the left of the image.

The Project... button is pressed to compute a projection.

Exercise 7
  • Produce a mean projection using every 2nd Z slice.

The allows you to toggle from colour to greyscale projection mode. Note in greyscale mode only one channel can be projected at the same time.

The icons allow you to toggle the individual channels on or off.

Exercise 8
  • Produce a projection using only one channel in greyscale mode.
  • Navigate the T dimension.

4.2.2 The Image Viewer Toolbar

The image viewer contains a toolbar which allows control over various advanced features. An overview of the tool bar is shown below.

We will for now ignore the measuring tool and the save as feature as these are covered in a later lessons. The selection of the data compression level is used to adjust the image quality. This feature is useful when viewing images over a slower internet connection.

4.2.2.1 The Render Settings

Return the viewer to Image mode by clicking on the Image tab. Next enable the render settings panel by clicking on the rendering control buttons. This will bring up a panel as shown below.

Using this panel it is possible to control the min/max threshold values for the channels using the sliders.
The sliders can also be set to the full range or to the automatically detected min/max range .
It is also possible to undo the last change and reset the sliders to their default states.
Pressing the icon allows you to see if any other users belonging to your group have viewed the image and allows you to view the image using the render settings they used.

Exercise 9
  • Adjust the render settings of the image using the sliders for each channel independently.

An important feature of the render settings is that the render settings can be copied from one image to another.
To do so you need to open an image with the image viewer, by selecting it in the workspace and double clicking it.
The render settings can then be adjusted for this image. The render setting can then be copied using the icon.
You can now close the image viewer and open a different image by double clicking it in the workspace.
You should see that the icon is enabled for this image. Press the paste icon to apply the render settings on the image.

Exercise 10
  • Adjust the render settings for one image, copy them, and then paste them to a different image.

Render settings can be saved using the icon. If the render settings have not been saved the viewer will automatically prompt you to do so upon closing the image viewer.

4.2.2.1.1 Advanced Render Settings

The advanced render settings features are available when pressing the icon in the render setting tab.This will reveal the panel shown below.

Using the advanced panel it is possible to control the brightness, reduce the bit depth, remove noise and adjust the gamma for individual channels.

Exercise 11
  • Adjust the brightness and apply the noise removal to one of the image channels.

4.2.2.2 Play Movie

The icon will bring up the movie player window shown below:

The movie window is useful to specify ranges of the Z and T dimensions for movie playback. The play mode can also be specified to allow for looping and more advanced behaviours.

Exercise 12
  • Try and reduce the Z and T ranges and produce a Back and Forth movie of your image.

4.2.2.3 Magnifying Glass

The icon is used to bring up the zoom window shown below:

This window allows you to control a virtual magnifying glass in order to view an enlarged area of your image. Parameters such as the size of the lens, zoom amount, units and lens colour can be changed using the top menu.

Exercise 13
  • Use the zoom window to create a 100x100 lens with 200% zoom for a region in your image.

4.3 Collaborative Viewing

OMERO allows for data sharing between users by specifying group permissions. A user may belong to one or more groups, and the data in a group may at most be shared with users in the same group on the same OMERO server. The degree to which their data is available to other members of the group depends on the permissions settings for that group. Whenever a user logs on to an OMERO server, they are connected under one of their groups. All data they import and work that is done is assigned to the current group and cannot be moved to another group. To specify the group you logging in as, the OMERO login screen has the a drop down box found above the username as shown below:

Groups must be created by the server administrator. Users can then be added by the administrator or by a group 'owner' assigned by the administrator. This would typically be the PI of the lab. The group owners or server administrator can also choose the permission level for that group. The permission level can be:

  • Private: All data in this group is only visible to the user who owns it and the group owners. The group owner can view the data for other group members but not make any edits (same as read-only behaviour).
  • Collaborative - Read-only: Users in groups with this permission setting can view each others' data, but cannot edit or annotate another user's data. You can view another users' images but not comment, rate or tag their images.
  • Collaborative: Users in a collaborative group can view and annotate the data belonging to other users. You can tag another user's images or use their tags to annotate your own images. You can add comments to their images and save your own rendering settings for each image. However, you cannot edit the names of their images, projects, datasets, tags etc.
The screen-shot below shows a user in several groups, including a collaborative group called Workshop. When logged in to OMERO.insight, user can switch the group on the fly using the group options found on the top of the OMERO.insight application as shown below:



By clicking on the group box, it is possible to view and switch to the various groups one belongs to.




Exercise 14
  • Try switching from the Workshop group to the default group and back to the Workshop group.

When users belong/switch to a collaborative group, such as the Workshop group, it is possible to view another user's images.
Clicking on the icon will bring up the list of users belonging to the group:



Selecting a user will then add the user's hierarchy to OMERO.insight



In a collaborative group you have the following modes of interaction with another user's data:

CAN DO:
Tagging:
You can add your tags to your images or another user's images
You can add another user's tags to your images, their images or another user's images
You can remove tags that you have added
Comments:
You can add comments to your images or another user's images
Rendering settings:
You can apply and save your own rendering settings to another user's images
This will not affect their rendering settings on their images
Deleting:
You can delete your Images etc even if they have been annotated by another user.
CANNOT DO:
You can't edit another user's Project, Dataset or Image names or descriptions
You can't remove Images from another user's Dataset, or remove Datasets (resp. Plate) from Projects (resp. Screen).
You can't add Images to another user's Dataset, or add Dataset (resp. Plate) to Project (resp. Screen)
You can't delete anything that belongs to another user
Tagging:
You can't remove a tag that another user has added, even if it is your tag on your own image
You can't edit another user's tag names or descriptions
Comments:
You can't edit any comments on any images. Comments are a historical record (same for all permissions levels).
Deleting:
You are not allowed to delete your own Tags that have been used by another user. This is because another user may have spent considerable effort tagging their own images with your Tags and this work would be lost if you are allowed to delete them.
Exercise 15
  • Try viewing another user's data and adding your own tag to their images.
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