2 Getting Data In

2.1 Launching OMERO.insight

• Locate the OMERO.insight icon on your desktop.
• Open OMERO.Insight by double clicking on the icon.

Upon launching OMERO.insight you will be presented with the OMERO login screen as described here.

2.1.1 Logging in

In your delegate pack you will have been given your OMERO login details. Fill in the username and password details in the appropriate sections. Once you have filled in your account details and selected the server from the server list, proceed to click on the LOGIN button.

2.2 Launching OMERO.insight Importer

In order to begin the import of images into OMERO you need to click on the OMERO.insight importer icon.

You are then presented with the OMERO.insight Importer Window

To import images with the OMERO.insight importer, the import process follows three steps of The File Selection, Location selection and Import.

2.3 The File Selection

Use the File Chooser panel to browse and select the images.

• Add the selected images to the Files to Import by pressing the icon.
• Single Image files can be removed from Files to Import using the icon.
• Alternatively the button can be used to remove all the image files from the import queue.

2.4 Location selection

Select the file(s) to import by pressing the icon when clicked on the location Selection window pops up as shown below.

OMERO uses a Project/Dataset hierarchy structure and so a new Project/Dataset can be created for each import or if available an existing Project/Dataset can be selected.

• The view for an existing project selection.



• Once the specific Project has been chosen the existing Dataset's available are shown under the chosen Project.





• Alternatively a new Project and/or Dataset can be created



Once the Project/Dataset has been created the selected images will reside in the import queue panel with the details of the files/folder the size of the file and its location within the chosen Project/Dataset.



2.5 New From Folder Import

The client importer also supports the ability for the chosen Dataset to reflect the chosen folder name. This is demonstrated in the case below where the folder 28-09-2001 experiment 1 has been selected with the option --New From Folder-- in the Dataset selection.



With this selection made when added to the import queue the Dataset created now takes on the folder name. In this screenshot below, the Dataset name is 28-09-2001 experiment 1. The confirmation of this action is displayed in the import queue panel with the information shown in the Project/Dataset and the information set in the tick box for folder as Dataset.



2.6 Import

When ready the image files can now be imported by clicking the import button.



On import, the Import tab will open as displayed below. The following information is presented in the Import tab:

• The number of files/folders imported
• The number of cancellations if any
• The import start time and the duration of the import.
• The names of any tags if any

On the completion of the import, the highlighted blue link takes you to the location of your imported images in the data manager





The import tab also displays the image thumbnail, double-clicking on it launches the Image Viewer.



Exercise 1
• Try importing an image.
• Try importing an image with the dataset with the same name as the folder it is imported from.

2.7 Options

File Naming

• Select an image for importing.
• Select The File Naming section allows to select the name of the imported images shown below



• Select the option of Partial Version + Files Name - This will result in a shortened version of the file name e.g. myImage.tiff
• Select the option Full Path + Files Name = This will result in a full version of a file name e.g. C:ScientificImages/Images/myImage.tiff
• The option directories before a file allows for a customised version i.e. the short version plus a number of leading directories e.g. Images/myImage.tiff
• Click on Import to Add the image the file name information can be viewed in the data manager.
Exercise 2
• Try importing an image with a Partial Version + Files Name.
• Try importing an image with a Full Path + Files Name.

2.8 Tagging on Import

The OMERO.Insight supports Tagging on Import. This feature can be found through the options setting.





• Once the tags have been added they may be viewed and removed from the list.



• On the completion of import, the tags will then be shown under the annotations panel in the Right-hand panel in the Data Manager.



Exercise 3
• Try importing an image with a tag.

2.9 Support for High Content Screening Formats

• OMERO supports the reading of several High Content Screening formats which are displayed in a Screnn - Plate - Well hierarchy. If you are interested in this type of data, please ask for more information