omero_LinkageToolbox: Linking with OMERO via drag and drop

To link your ELN object with OMERO, simply drag and drop or paste the URL of your ELN object onto the selected elements in OMERO (such as Datasets or Images). This action prompts OMERO to send a *.eln file containing the metadata of all associated images to your ELN, creating a new ELN entry linked to your chosen ELN object.

To incorporate data bridging into your infrastructure, please follow the steps outlined below.

Supported ELN platforms

• openBIS version >=20.10.8

Prerequisites

Check your Python installation on omero-server:

• Python version >=3.9;

• make sure the following Python modules are installed on your omero-server:

  omero-py (tested with v5.19.5)
  rocrate (tested with v0.11.0)
  

Installation

Definitions:

• $ELN_INSTANCE_DIR is the path on the e.g. eln-server where your eln is installed (e.g. /home/openbis/openbis/).

• $ELN_SHARE is the watch folder on your eln-server (e.g. /home/openbis/dataBridge_omero)

The omero_LinkageToolbox allows you to combine your OMERO instance with any of the supported ELN platforms. Follow the steps for both OMERO and your chosen ELN platform

Steps for OMERO:

1. Mount ELN share $ELN_SHARE as $DROPBOX_MNT

2. Download the ELN_Writer.py script and edit its configuration section:

   # the output path for building the .eln file 
   OUTPUT_PATH = "/tmp"
   # the ELN Share receiving the .eln files
   ELN_SHARE = §DROPBOX_MNT
   # the url of your ELN instance
   ELN_URI = "https://myELN.de"
   # the url of your OMERO instance
   OMERO_URI = "https://omero.institute.de"
   

3. Upload the script ELN_Writer.py to your omero instance (see the “HowTo upload a server-side script in OMERO” guide) in order to run it as a server-side script.

4. On omero-server check if all Python modules listed in required modules are installed

Steps for openBIS:

1. To create a dropbox, navigate first to $ELN_INSTANCE_DIR/servers/core-plugins and create a directory structure for your dropbox (for example, creating the directory structure dataBridge/1/dss/drop-boxes/omero-dropbox)

   cd $ELN_INSTANCE_DIR/servers/core-plugins/
   mkdir -p dataBridge/1/dss/drop-boxes/omero-dropbox
   

2. Copy omero-receiver.py to the omero-dropbox folder and specify EMAIL_FROM and EMAIL_TO to send a notification mail to the dropbox administrator if any issues arise during operation.

3. In the omero-dropbox directory, create and configure the plugin.properties file (see plugin.properties for details)

4. Add your core-plugin (e.g. dataBridge) to the list of enabled-modules in $ELN_INSTANCE_DIR/servers/core-plugins/core-plugins.properties

5. Don’t forget to create the watch folder $ELN_SHARE on your openBIS-server

   cd /home/openbis/
   mkdir dataBridge_omero
   

6. Configure $ELN_SHARE as SHARE and grant omero-server write access to that folder

7. Restart DSS server

   After the restart the dropbox should be listed in the eln-lims GUI under Dropbox Monitor.

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Usage

1. Click on /select the dataset or images you want to link with the omero_LinkageToolbox.

2. Click on OMEROs script button and choose the script ELN_writer.

3. The ELN_writer will open in a new window. If pre-chosen, the dataset or image IDs and their data type are already written to the “IDs” and “Data Type” field. Otherwise type in all IDs you want to link and select the corresponding data type. If you choose Dataset: Pay attention to the ELN link option, which defines if you want a link to the ELN experiment on all images in the dataset or solely on the dataset itself. Choose which metadata to include in the linkage. Don´t forget to paste or drag and drop the ELN url! Finally “Run script”.

If your ELN is openBIS:

An entry with the name „OMERO data“ will be created and linked to your pasted /drag&drop object.

Results in preview mode:

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