Basic Operations

• Navigate between groups

  • Switching to a different group

  • Switching to view images of another member of the same group

  • Accessing another member of another group

• Creating a new project and a new dataset

• Moving images to projects and datasets

• Renaming projects, datasets and images

• Renaming channels

• Previewing images with rendering settings

Step-by-Step

Navigate to a different group

1. On the right-hand side panel, choose Group Training_2025b

   

2. Select Training_2025b and select your name under Member

3. You should see that the group that you are viewing on the right-hand panel has changed.

4. Switching to view other member (someone sitting next to you) of Training_2025b

5. Switching to view one of your colleagues of your Lab-<group>

Accessing project and dataset

1. Switch to Group Training_2025b and viewing your project, dataset and images

2. There is a Project named omero_training.

3. Within project omero_training, you will find a dataset.

4. Click on the dataset, you should see a set of images underneath it.

• In OMERO, names are not unique, instead everything has an ID.

Creating a new project and a new dataset

1. Switch to Group Training_2025b and viewing your project, dataset and images

2. Right-click on your name and a drop-down menu will appear.

   

3. Create a project named “ProjectA” and a dataset with named “dataset1”

Moving images to a different project and dataset

1. Choose an image from project “omero_training” and move that into dataset1

2. Choose another image and move it to be under ProjectA

Copying images (i.e. Copy Link)

1. Copy Images using the right-click context menu:

   • Select the Images to be copied, then right-click and click Edit > Copy Link.

   • Select the Dataset you want to copy the Images to, right-click and click on Edit > Paste Link.

     

Warning

The Copy Link feature will only create new links between an Image and a Dataset, so that one Image becomes linked to multiple Datasets. This does not create a new independent copy of the Image. The only way to create a fully independent copy in OMERO is to use the Duplicate feature (see below).

If you delete one of the Datasets, any Images within it that are linked to other Datasets will be retained. Nevertheless, if you directly select and delete an Image that has been copied from another Dataset it will be deleted and lost from both Datasets. There is a clear warning in the OMERO.web when you try to delete such a doubly linked Image, see screenshot below.

Renaming image

1. Choose the previous image that you put in dataset1.

2. Renaming the image by going to the left-hand panel.

   

3. Rename it as imageA

4. Choose another image from omero_training and rename that to imageA

• As you can see, there are two images with the same name. OMERO does not treat names as unique.

Move data between groups

In OMERO, Users are organized in Groups. The Groups allow a level of viewing and cooperation between the members of the group which can be adjusted by changing the permissions level on that group. A User can be a member and have their data in one or more Groups. Thus it is sometimes necessary to move the data between groups. This action can be done by the owners of the data themselves or by an administrator or an administrator with restricted privileges.

Note that caution has to be taken in case the data are linked to other users’ containers (Datasets, Projects). If you move only the contents of those containers (Datasets or Images) and not the containers themselves (Projects or Datasets), the links between such containers and the Images or Datasets which are moved will be deleted.

Further, if any objects are moved, the links to any annotations such as Tags or attached File annotations linked to these objects will be deleted in case these annotations belong to others or in case these annotations belong to you but are also linked to some other objects in the original group which are not being moved.

If you want to retain a copy of your data in its current position, then you should Duplicate it. The Duplication also bypasses the unlinked annotations problem highlighted in the previous paragraph. Because the Duplicate feature creates new objects, which are not dependent on the originals, the relationships between these duplicates are then preserved even during a subsequent move to another group.

Contact Ken Ho if you want to duplicate your projects, datasets or images

Move data between groups: owners of data

If you are an owner of the data, you can move the data between the groups you are a member of.

1. In OMERO.web, select the data to be moved in the left-hand side tree.

2. Right-click and select Move to Group....

   

3. Select the group you want to move the data to.

4. A message Checking which linked objects will be moved will appear and a spinner to the left of it. Wait until the spinner vanishes and a list of objects to be moved and a list of objects which are not included in the move appears.

   

5. Check both lists. Please read the note above about which objects are typically not included and reconsider the Move action. The not included objects will not be linked to the Moved objects anymore if you go ahead with the move, the linkage will be lost.

6. In case you are happy with the Move``action to go ahead, select a target Dataset or Project or create a new one and click ``OK.

Righ-hand Pane

1. Select an Image. In the right-hand pane, metadata read by Bio-Formats and stored in a relational database is displayed:

   • Core metadata in the General tab.

   • Additional metadata in the Acquisition tab.

   • All the metadata read by Bio-Formats can be downloaded at any time.

2. In the Preview tab in the right-hand panel, you can also view the Image.

3. For multi-plane Images, sliders allow you to move through Z or Time dimensions.

4. Viewing Images does not download the whole Image to the client. Only the viewed Image plane is rendered from the original Image file on the server and sent back to the OMERO.web client.

Renaming channels

1. Choose an image and click at the General tab on the right hand panel.

2. Click on the pencil-like icon at the end of the row Channels:

#. You will find a channel edit window open within the righthand panel. # Select any image inside that Dataset and click on the pencil icon in the right-hand pane next to Channels.

- Input “DAPI” instead of channel “457” and “GFP”, “Aurora-B” and “CY-6” for the other channels.

• Click the Apply to All button and confirm by clicking Continue. This will change the channel names of all the images in that Dataset.

Preview rendering setting

1. Choose an image and click at the Preview tab on the righ hand panel.

2. You will see an image viewer on the right hand panel displaying your image and channel settings.

3. Adjust the channel and you can save the settings by clicking at the Save icon.

4. Click on the Show Histogram checkbox, it will display a histogram of the 1st channel.

5. You can click on other channel to display their historgrams.

6. You can undo the settings by clicking on the icon undo

7. The rendering settings can be saved to the server. This never changes the original Image data and can be reverted at any time.

8. The rendering settings can also be copied and pasted between Images.

9. To modify the rendering settings in batch, click on the Save to All button to apply the same settings to, for example, all Images in a given Dataset.

10. You can use the settings which other users saved on your Images and apply them for your own Image. These settings are highlighted as thumbnails in the lower part of the Preview pane.

11. You can adjust the rendering settings for each channel e.g. turn on/off the channels, adjust color settings, look-up tables, etc.

12. You can use the settings which other users saved on your Images and apply them for your own Image. These settings are highlighted as thumbnails in the lower part of the Preview pane.

13. Your own settings are highlighted in blue.

14. You can revert to the original settings for an Image or Dataset. For example, using the context menu for a Dataset in the tree, select Rendering Settings > Set Imported and Save.