=Description=
We will show:
- How to open an image from EPFL-OMERO server in QuPath and load the ROIs from OMERO on that image
- How to draw annotations and perform simple Cell detection in QuPath
- How to export the ROIs from QuPath as OME-XML
- How to import the OME-XML to the OMERO.server and attach the QuPath ROIs to the original image in OMERO
= Resources =
Plugin `ome-omero-roitool v0.2.2` for import and export of ROIs to or from OMERO using OME-XML format:
[[ https://github.com/glencoesoftware/ome-omero-roitool | https://github.com/glencoesoftware/ome-omero-roitool ]]
The `ome-omero-roitool-xxx.zip` under `Releases` also contains the scripts for export and import of ROIs from/to QuPath in OME-XML format. For precise installation steps, see below the Step-by-step section.
=Step-by-step=
**In the following steps, we will show how to open an image from the OMERO server in QuPath, load the ROIs from OMERO on that image, and perform simple Cell detection in QuPath**
# Open your Image in OMERO.web with the OMERO.iviewer. In the OMERO.iviewer tab, select the whole URL in the address bar of your browser and copy it, for example using right-click and `Copy`
# In QuPath, create a new Project `File > Project > Create Project` or open an existing one `File > Project > Open Project`.
# Once the Project is open, click the `Add Images` button above the left-hand pane in QuPath.
# In the following dialog, check the `Import objects` checkbox. This tells QuPath to import all ROIs on that image from OMERO into QuPath. Note though that masks will not be imported.
# In the same dialog, click the `Input URL` button. {F16828655}
# Paste the link to the image you copied from the OMERO.iviewer tab (see above) into the dialog. {F16828667} Click `OK`.
# Enter your gaspar credentials. Click `Import`.
# The image thumbnail will appear in the left-hand pane list of the QuPath Project. Click on that thumbnail to open the image in QuPath’s full viewer.
# Set image type and click `OK`.
# Find your ROIs from OMERO now in QuPath on that image.
# To draw new ROIs or annotations in QuPath, find a region with well-defined cells and nuclei in the image, zoom in. Draw an ROI Annotation which denotes the region in which the cells will be detected using the Wand tool. Adjust your ROI Annotation using the Brush tool.
# Select `Analyze > Cell detection > Cell detection`. You can adjust the parameters. Click `Run`. This will draw red ROIs around cells and nuclei inside your ROI Annotation.
# Select `Measure > Show detection measurements`.
# Note: You can save the results locally by clicking `Save` in the bottom right of the `Detection results table`.
**In the following steps, we will show how to convert the ROIs your just created in QuPath into OMERO ROIs and attach them to the image in OMERO.**
# First, use the `ROI OME-XML` export script to export your ROIs from QuPath into OME-XML file. Find the version of `ome-omero-roitool` mentioned in `Resources` on `ome-omero-roitool` releases and from there download the `ome-omero-roitool-xxx.zip`. The downloaded zip contains both the plugin and the QuPath scripts needed for this workflow.
# Unzip the downloaded artifact and drag and drop the `OME_XML_export.groovy` into your QuPath. Run the script by selecting select `Run > Run.` Note: If you run a Cell detection in QuPath, the nuclei ROIs will be drawn as well as the ROIs around the cells. The ROI OME-XML export script will export both the ROIs around the cells as well as the nuclei ROIs.
# Import the OME-XML with the ROIs from QuPath into OMERO. These steps must be run on a command line. Open your terminal window.
# Unzip the downloaded file and go into the resulting folder as follows:
```
unzip ome-omero-roitool-xxx.zip
cd ome-omero-roitool-xxx
cd bin
```
On Mac or Linux, run:
```
./ome-omero-roitool import --password GASPARPASSWORD --port 4064 --server omero.epfl.ch --username GASPARUSERNAME IMAGEID PATH/TO/OME-XML/FILE/export.ome.xml
```
On Windows, run:
```
ome-omero-roitool import --password GASPARPASSWORD --port 4064 --server omero.epfl.ch --username GASPARUSERNAME IMAGEID PATH\TO\OME-XML\FILE\export.ome.xml
```
After you executed the import command above, go to OMERO.iviewer in your browser and view the ROIs on the image. The `Annotation` from QuPath is displayed as a mask ROI in OMERO.iviewer. Masks cannot be edited in OMERO.iviewer at the moment, but they can be viewed. The mask, when selected displays a blue bounding box around the `Annotation` on the image.