= 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 client is required to import images to OMERO.
=== At the BIOP ===
{F17946695, float, height=60} The OMERO.insight client 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.
== 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}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.
== 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 ]]
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{icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/viewing | NEXT STEP: Viewing data ]]
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