Phriction Projects Wikis Bioimaging And Optics Platform Image Processing OMERO Importing (and downloading) images History Version 11 vs 12
Version 11 vs 12
Version 11 vs 12
Content Changes
Content Changes
= 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.epfl.ch} into the line.
{F17940907, height=300}
- **Enter your gaspar credentials**
The first time you login, please clic on the lock to close it
{F7111871, height=300}
You are now successfully connected
{F7111889}
== Create Project ==
Select your username and {nav Right-Clic > Create New >New Project ...}
{F7111898}
Specify name and press {key Create}
{F7111919}
Your project is created
{F7111908}
== Create Dataset==
Select a project and {nav Right-Clic > Create New >New Dataset...}
{F7111940}
Specify name and press {key Create}
{F7111951}
Dataset is created
== Import Images ==
Select a dataset and {nav Right-Clic > Import...}
{F7111960}
- Select Images, then Press {key >}
{F7111987}
- Project and Dataset should allready be correct and Press {key Add_to_the_Queue}
{F7112002}
- The list is updated , press {key Import}
{F7112017}
- Images are added to the dataset
{F7112297}
- Slider at the bottom to enlarge images
{F7112309}
- Double-clic on an thumbnail open a new window
{F7112323}
= 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.epfl.ch} into the line.
{F17940907, height=300}
- **Enter your gaspar credentials**
The first time you login, please clic on the lock to close it
{F7111871, 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 {navSelect 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}
Your project is created
{F7111908}
== Create Dataset==
Select a project and {nav Right-Clic > Create New >New Dataset...}
{F7111940}
Specify name and press {key Create}
{F7111951}
Dataset is created
== Import Images ==
Select a dataset and {nav Right-Clic > Import...}
{F7111960}
- Select Images, then Press {key >}
{F7111987}
- Project and Dataset should allready be correct and Press {key Add_to_the_Queue}
{F7112002}
- The list is updated , press {key Import}
{F7112017}
- Images are added to the dataset
{F7112297}
- Slider at the bottom to enlarge images
{F7112309}
- Double-clic on an thumbnail open a new window
{F7112323}
= 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.epfl.ch} into the line.
{F17940907, height=300}
- **Enter your gaspar credentials**
The first time you login, please clic on the lock to close it
{F7111871, height=300}
You are now successfully connected
{F7111889}
== Create Project ==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.
Select your username and {nav Right-Clic > Create New >New Project ...}When ready click on {nav Import}.
{F7111898}{F17947258, size=full}
Specify name and press {key Create}6. Import progress will be shown in the {nav Import #1} tab.
Further data can be queued and imported using the {navSelect 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.
{F7111919}{F17947278, size = full}
Your project is created
{F7111908}
== Create Dataset==
Select a project and {nav Right-Clic > Create New >New Dataset...}
{F7111940}
Specify name and press {key Create}
{F7111951}
Dataset is created
== Import Images ==
Select a dataset and {nav Right-Clic > Import...}
{F7111960}
- Select Images, then Press {key >}
{F7111987}
- Project and Dataset should allready be correct and Press {key Add_to_the_Queue}
{F7112002}
- The list is updated , press {key Import}
{F7112017}
- Images are added to the dataset
{F7112297}
- Slider at the bottom to enlarge images
{F7112309}
- Double-clic on an thumbnail open a new window
{F7112323}
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