OMERO Usage Tutorials
OMERO is “client-server software for visualization, management and analysis of biological microscope images” developed by the Open Microscopy Environment (OME) consortium. The OMERO platform consists of a server, several desktop clients, and a web-based client. Experimenters can access their data either via the OMERO.insight desktop client or via the OMERO.web webclient. Both OMERO.insight and OMERO.web allow experimenters to access, organize, annotate, visualize, and share data with collaborators.
At LOCI, the Optical Workstation (OWS) and WiscScan software have been configured to automatically transfer acquired data to the OMERO server where it can be accessed using both the desktop and web clients. This automation allows OWS users to take advantage of OMERO’s features with few additional steps to the existing OWS workflow.
- Uploading Data
- Accessing Data
- Browsing and Searching Data
- Annotating Data
- Sharing Data
- Exporting Data
Uploading Data into OMERO
Automated uploading (not yet available):
- On the OWS, log in to WiscScan using your UW NetID and password.
- Log in to Samba using your UW NetID and password.
- Acquire data in WiscScan as you would normally.
- When prompted, save your data to your Samba folder (the name of this folder will be the same as your UW NetID).
- Data saved to your Samba folder will automatically sync to the OMERO server using the OMERO DropBox feature.
Manual uploading via OMERO.importer:
- Launch and log in to OMERO.importer.
- Select the files you want to import in the left pane.
- Click the "+" button. This will open the "Image Import" pop-up window.
- In the pop-up window, select the Project and Dataset where you want to import your images (new Projects and Datasets can be added by clicking the "Add" buttons").
- Make sure to check the box next to "Archive the original imported file(s) to the server".
- The files you selected should now appear in the right pane. Click "Import" to begin uploading the files.[img_assist|nid=790|title=Uploading data with OMERO.importer|desc=|link=none|align=center|width=700|height=389]
Accessing Data in OMERO
Via the OMERO.insight desktop client:
- Download and install the OMERO Clients (available for Windows, Mac, and Linux).
- Open the OMERO.insight client.
- Enter open.microscopy.wisc.edu as the server name (you should not have to change the port).
- Choose your group (“loci” is the default, but others can be created as needed).
- Log in using your UW NetID and password.
- Go to http://open.microscopy.wisc.edu/webclient/
- Log in using your NetID and password.
Browsing and Searching Data in OMERO
Data are organized in OMERO according to the OME data model. This hierarchical model includes Project, Dataset, and Image levels (multiple Images can belong to a Dataset and multiple Datasets can belong to a Project). Images are imported into a single Project and Dataset, but can be edited and reorganized after import.
There are multiple ways to browse and search data in OMERO. Both OMERO.insight and OMERO.web allow browsing; however, the interfaces and available features differ.
Browsing/searching data in OMERO.insight:
- Browsing by hierarchy (Project/Dataset/Image), owner, tags, and upload date is available in the left pane. As you browse through the above categories, the appropriate thumbnails will appear in the center pane and metadata will appear in the right pane.
- Searching is done in the left pane below the browsing options. The search feature consists of a single field and check-boxes for limiting searches to names, descriptions, comments, tags, and attachments.
- The default search (no limit boxes checked) covers all text including names, comments, tags, and some imported metadata.
- Clicking the yellow arrow under the search box provides advanced search options allowing the user to look for an exact phrase or to exclude certain words.
- Wildcards can be used in any of the search fields (*.lei would return any file ending in .lei).
Browsing/searching data in OMERO.web:
- The web client homepage contains browsable images, tags, and comments from the most recently imported data.
- Clicking the “Data” icon at the top of the screen takes the user to a page where they can browse all of their data by hierarchy (Project/Dataset/Image) or by tags.
- Clicking the “History” icon at the top of the screen takes the user to a screen where they can browse their data by upload date.
- Clicking the “Search” icon at the top of the screen takes the user to a page where they can search within Images, Datasets, Projects, Plates, and Screens (at least one of these must be checked for the search to work.
Annotating Data in OMERO
Annotations can be added in both OMERO.insight and OMERO.web at the Project, Dataset, and Image levels.
Annotating data in OMERO.web:
- Select the Project, Dataset, or Image to be annotated.
- In the right pane, click the “Annotation” link and then click the green pencil icon in the “Comments” section. This will bring up a screen where free text comments can be entered.
- After saving the comment, click on the “Annotation” link again, and the new comment should appear.
- Click the green pencil icon in the “Tags” section. This will bring up a screen where a tag (keyword) can be added to the image. An optional description of the tag can also be entered for each tag. In addition to creating new tags, existing tags can be used (including tags created by other members from collaborative groups). Tags can be searched and browsed in both OMERO.insight and OMERO.web.[img_assist|nid=785|title=Annotation screen in OMERO.web|desc=|link=none|align=center|width=577|height=358]
Annotating data in OMERO.insight:
- Select the Project, Dataset, or Image to be annotated.
- In the right pane, find the “Annotations” section.
- To add a comment, click in the “comment” field and enter text.
- To add a tag, click the “+” next to “tag.” This will open a pop-up window with a list of existing tags. Select tags from the left pane and move them to the right pane using the “>” button (the “<” button returns them to the left). Click “Accept” to add the tags from the right pane to the Project, Dataset, or Image. New tags can be added using the text field at the bottom of the pop-up window.
- To add a rating, click on the stars next to “rate.” Ratings range from 1 to 5 stars (ascending from left to right).[img_assist|nid=787|title=Annotation screen in OMERO.insight|desc=|link=none|align=center|width=548|height=410]
Sharing Data in OMERO
NOTE: There are three levels of permissions for groups in OMERO (Private, Collaborative Read-only, and Collaborative). Only the two Collaborative settings allow sharing. The “loci” group is currently set to Collaborative. Users can belong to more than one group and can switch between groups in both OMERO.insight (drop-down near top left) and OMERO.web (drop-down near top right).
Accessing other group members’ data in OMERO.web:
- Log in to OMERO.web.
- Click on the “Data” icon in the main navigation menu (upper right).
- Click on the experimenter drop-down menu (top-left) to see a list of all members in the group (see below).
- Select any member of the group to view and annotate their data (note: annotations are only allowed in Collaborative groups).
- Data belonging to other users is searchable and browsable using the same methods described in the previous section.[img_assist|nid=788|title=Sharing data in OMERO.web|desc=|link=none|align=center|width=701|height=385]
Accessing other group members’ data in OMERO.insight:
- Launch OMERO.insight.
- Click the icon showing what appears to be two faceless people located next to the drop-down menu for selecting groups (see below).
- A window will pop up with a list of all of the group members.
- Click on any group member and click “Apply” to add that user’s data to the “Hierarchies” pane (left side). Repeat this process if adding data from several users.
- Once added, the other users’ data is browsable and searchable using the same techniques described in the previous section.[img_assist|nid=789|title=Sharing data in OMERO.insight|desc=|link=none|align=center|width=701|height=437]
Exporting Data from OMERO
Data can be exported from OMERO.insight two different ways, and each method has its own benefits and drawbacks:
- To export an OME-TIFF file with all of the annotations added in OMERO included in the metadata, select an image and click the "Export the image as OME-TIFF" icon in the metadata pane (see below). NOTE: The metadata embedded in this file will not include all of the metadata WiscScan captures, but it will include any annotations added in OMERO.[img_assist|nid=791|title=Exporting images as OME-TIFF|desc=|link=none|align=center|width=700|height=474]
- To export the original OME-TIFF file you imported into OMERO, select an image and click the blue arrow icon in the metadata pane (see below). NOTE: The metadata embedded in this file will not include any annotations added in OMERO, but it will include all of the original metadata from WiscScan.[img_assist|nid=792|title=Exporting original imported files|desc=|link=none|align=center|width=700|height=474]