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Introduction

OMERO stores image data on a central server. You can use the OMERO.insight client to upload, view and download data from any personal computer.

Your institution’s OMERO server administrator will provide you with the server address to use when connecting from OMERO.insight. They may have set up a user name and password for you too. Alternatively your username and password may be your standard login for the institution’s networked computers.


Installing

  1. Download the OMERO.insight client at: https://www.openmicroscopy.org/omero/downloads


    ../images/gettingStarted5Downloads.png

  2. Expand OMERO.insight client archive and move it to your home directory.


    Windows:

    ../images/gettingStarted5ZipsWin.jpg

    Mac OS X:

    ../images/gettingStarted5ZipsMac.jpg

    Linux:

    ../images/gettingStarted5ZipsLinux.jpg

  3. Open the OMERO.insight client.


    ../images/gettingStarted5Apps.jpg

    Note

    Mac users may be blocked by a warning that OMERO.insight has been prevented from opening as it is from an unidentified developer.

    Follow these instructions to adjust the security settings so OMERO.insight can run on your Mac:

    OS X Mavericks: Open an app from an unidentified developer



Adding server and logging in

Adding the server is only required the first time an OMERO server is accessed from the computer.


  1. Click on the wrench icon.


    ../images/gettingStarted5Spanner.jpg

  2. In the Add Server dialog box, click on the + icon.


    ../images/gettingStarted5Add.jpg

  3. Enter the server address provided by your OMERO administrator.

    Click on Apply.


    ../images/gettingStarted5Apply.jpg

  4. Enter the Username and Password provided by your OMERO administrator.

    Click on Login.


    ../images/gettingStarted5Login.jpg

Adding image data

  1. Click on the Importer icon.


    ../images/gettingStarted5DataManager.jpg

  2. Add image data using the File Chooser.


    ../images/gettingStarted5FileChooser.jpg

  3. Select image data to be imported.

    Click the right Add arrow.


    ../images/gettingStarted5Data.jpg

  4. Specify a location for saving imported data:

    - select a group if you are a member of more than one

    - a new project and/or dataset can be created

    - an existing project and/or dataset can be selected from the drop-downs

    - a new dataset can be automatically created from the source folder

    - click Add to the Queue


    ../images/gettingStarted5Project.jpg

  5. Data to be imported appears in queue pane.

    When ready click on Import.


    ../images/gettingStarted5Import.jpg

  6. Import progress will be shown in the Import # 1 tab.

    Further data for import can be queued and imported using the Select Data to Import tab.

    Multiple queues can be run simultaneously.

    A green check is shown in the import tab and in the top right corner of the main Data Manager window when the queue is successfully imported.


    ../images/gettingStarted5Complete.jpg

  7. Double-click on the thumbnail or select from the View menu to open the image in the full viewer.


    ../images/gettingStarted5Close.jpg

  8. Click the Refresh button to see the imported data in the data manager.

    Import progress is shown by a green tick on the right-hand side of the data manager window toolbar.

    Notifications of any import failure will also appear there with a red X.


    ../images/gettingStarted5ImportedData.jpg



Viewing image data

  1. The Data Manager window is divided into 3 panes:

    - the left hand pane shows the data tree and tabs for screens, attachments, tags and search

    - the center pane shows thumbnails and enables filtering of images

    - the right hand pane shows the general information, metadata and the preview


    ../images/gettingStarted5Panes.jpg

  2. Double click the image name or thumbnail to open an image in the full viewer or click on the image viewer icon.


    ../images/gettingStarted5View.jpg

  3. The image viewer enables you to change rendering settings.

    Hide / show rendering settings pane.

    Toggle between color and monochrome rendering.


    ../images/gettingStarted5Rendering.jpg

  4. Click the color picker to open the color picker window.

    Select a color or color lookup table (LUT) to change the color rendering for a channel.

    Clicking the color well toggles the channel on or off.


    ../images/gettingStarted5Picker.jpg

  5. Click on Metadata button to view the metadata in the right pane.


    ../images/gettingStarted5Metadata.jpg

  6. Click on Measurement Tool button to open the Measurement Tools palette.


    ../images/gettingStarted5ROI.jpg

  7. Use the toolbar to draw Regions of Interest (ROIs).

    Click on the tabs to see details of ROIs or view results of analysis based on them.


    ../images/gettingStarted5Tools.jpg

  8. Use the sliders to step through Z-stacks and T-sequences or click the Play triangle to play through them as a sequence.


    ../images/gettingStarted5Stacks.jpg


All Tutorial Material is available on line at: help.openmicroscopy.org

The Main OME website is at: www.openmicroscopy.org