= OMERO.insight = Although images can be viewed from anywhere you have internet access by connecting to the webclient ([[https://omero.epfl.ch/webclient/ | omero.epfl.ch]]), the OMERO.insight desktop application is required to import images to OMERO. === At the BIOP === {F17946695, float, height=60} The OMERO.insight desktop application has been installed and configured on most of the BIOP's microscope computers (you can find the list [[https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/biop/ | here ]]). It can be accessed via the {nav EPFL - OMERO} desktop shortcut, which is available for every EPFL users. Enter your gaspar credentials to log in. === On your computer: OMERO.insight installation and configuration === - **Download OMERO.insight** First, you need to find the [[ https://www.openmicroscopy.org/omero/downloads/ | omero desktop client]] compatible with your Operating System (OS), either Windows, Mac OS X, Linux. {F17940836, size=full} After the installation, please follow the simple steps below: - **Launch OMERO.insight** {F17940867, height=300} - **Define the server adress** In the login dialog, click on the wrench icon. This will open a list of servers to which you can connect. By default, only {nav localhost} is listed. Click on the plus icon to add a new line to the list and type {nav omero-server.epfl.ch} into the line. {F18510795, height=300} - **Enter your gaspar credentials** The first time you login, please clic on the lock to close it {F18510811, height=300} You are now successfully connected {F7111889} == Import images == 1. Go to {nav File > Import}; **or** Click on the Import icon in the toolbar; **or** Select a destination Project or Dataset for the imported data, right click and select {nav Import}. {F17947110, size=full} 2. Use the File Chooser to locate data to be imported on local or networked drives. {F17947203, size=full} 3. Select image data to be imported. Click the right **Add** arrow. {F17947208, size=full} 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 {nav Add to the Queue} {F17947217, size=full} 5. Data to be imported appears in the queue pane. When ready click on {nav Import}. {F17947258, size=full} 6. Import progress will be shown in the {nav Import #1} tab. Further data can be queued and imported using the {nav 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. {F17947278, size = full} (IMPORTANT) Please look at the //[[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/file-formats/ | How to import to OMERO depending on the file-format ]]// guide to learn how to upload more complex data types (i.e screening data) to OMERO. == Import for another user == **If you are an OMERO Group Owner** , you can use the {nav Import For} drop-down box to select another user to import the data as. The chosen user will then own this data. The Project and Dataset drop-down boxes list the projects and datasets available for the selected user to import into. {F20210790, size = full} == Add voxel size at import == If a file do not contain voxel sizes in its metadata, they can be added manually during the upload to OMERO. This can be done under the {nav Options} tag from the right panel of the OMERO.insight client. {F19856553, size=full} == Create a new Project == Go to {nav File > New > icon=folder, name = New Project... } **or** Right-clic on your name and select {nav Create New > icon=folder, name = New Project...} Specify name and press {nav Create} {F7111919, size = full} == Create a new Dataset== Right-clic on a project and select {nav Create New > icon=folder, name = New Dataset...} Specify name and press {nav Create} {F7111951, size = full} = Download or export images from OMERO = ===** Download images using OMERO.web ([[https://omero.epfl.ch/webclient/ | omero.epfl.ch]]) **=== {F19857897, size = full} ===** Download larger files using the OMERO.insight desktop application**=== {F19857898, size = full} ===** Export a subset of Z/T sections using the Batch image export script in OMERO.web **=== {F19857899, size = full} = More documentation on this topic... = To learn more about importing images to OMERO, we recommend you to visit the [[ https://omero-guides.readthedocs.io/en/latest/upload/docs/import-desktop-client.html | dedicated page from the official OMERO guide ]] or [[https://downloads.openmicroscopy.org/help/pdfs/importing-data-5.pdf | this nice step-by-step PDF tutorial ]] --- {icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/viewing | NEXT STEP: Viewing data ]] ---

https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Importation https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Exportation