Phriction Projects Wikis Bioimaging And Optics Platform Image Processing OMERO Importing (and downloading) images History Version 22 vs 25
Version 22 vs 25
Version 22 vs 25
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 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 ]]
---
{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/Installation
https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Importation
https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Exportation
= 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.
== 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/Installation
https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Importation
https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Exportation
c4science · Help