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Fiji

Fiji image analysis for OMERO

While an official OMERO plugin for Fiji exists, which allows to load images from OMERO directly in Fiji and upload results and ROIs back to OMERO, at Leiden University we have our own developed plugin, which allows to directly run developed Fiji scripts/plugins on images in OMERO.

By following the steps below, you can install the required plugins and run your analysis on images in Fiji.

Installation Steps

  1. Install Fiji
  2. Update Fiji and ensure all plugins are up to date (Help > Update)
    • If you get errors, repeat the update (the updater might need multiple attempts)
    • After seeing "Updated successfully. Please restart ImageJ!" message, restart Fiji

Update success message

  1. After restarting, update again and click "Manage Update Sites"

Manage update sites

  1. Enable these required sites:
    • Fiji legacy
    • 3D Image suite
    • ImageScience
    • Leiden University
    • PTBIOP

Update sites selection

  1. Click Close and Apply Changes
  2. Restart Fiji
  3. Install the Simple OMERO Client:
    • Download from GitHub releases
    • Place in Fiji's plugins folder
    • Restart Fiji

Analysis Methods

Manual Single Image Analysis

  1. Open OMERO connection:

    • Go to Plugins > OMERO > Connect to OMERO
    • Login with ULCN credentials
    • OMERO.insight connected to Fiji will open

  2. Access your image:

    • Locate image in left sidebar or thumbnails
    • Double-click to open

  3. Configure BioFormats Import:
    BioFormats import options

    • Adjust settings as needed
    • Click OK
    • Wait for loading (may take several minutes, no progress bar visible)

Dataset Analysis

Manual Dataset Analysis

  1. Launch dataset opener: - Go to Plugins > LeidenUniv > OMERO > Open OMERO dataset - Enter login credentials: Login screen

  2. Select dataset:
    Dataset selection
    - Choose group, user, project, and dataset - Click OK

  3. Monitor progress:
    Loading progress
    - Watch log window for loading progress

  4. Analyze your data creating either: Resultstables ROIs Images

  5. Upload results to OMERO via Plugins>Omero> Save results to OMERO Save Rois to OMERO Save Image(s) to OMERO

Automated Dataset Analysis

  1. Start automated analysis:

    • Go to Plugins > LeidenUniv > OMERO > Run OMERO plugin
    • Enter login credentials: Login screen

  2. Choose Plugin to run:
    Choose Plugin

  3. Select dataset:
    Dataset selection for automation

  4. Optionally set plugin parameters

  5. View results after the plugin finishes:

    • Results attach to image/dataset automatically
      Log
      Results attachment Detailed results

Exporting Data

Within the Leiden University Fiji plugin there are several options available to download images from OMERO.

Leiden OMERO Plugin options

In all cases you will be asked to enter you OMERO credentials.
Enter OMERO credentials

Download Dataset as TIFFs

This option will download all images in the dataset as TIFF files to your local machine. You can select the dataset you would like to download and select a destination folder where the images will be saved.

Download Original Project Data

This allows to download the original data, in the original file format of a project. You can select the project you would like to download and select a destination folder where the data will be saved.

Detailed results

Download Original User Data

This option allows to download all the original data of a user, in the original file format. Be aware that when you have a large amount of data on OMERO this can take a long time to download. You can select the user you would like to download and select a destination folder where the data will be saved.

Info

If you need a plugin that isn't available, contact Joost Willemse for assistance.