2024_OMERO_Basic_Upload

imaging-omero-suite/2024-omero-basic-upload

Author(s)
Riccardo Massei
Version
1
Last updated
Mar 5, 2026
License
CC-BY-4.0
Tags
imageanaylsis
NFDI4Bioimage
OMERO
RDM

Features
Tutorial
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nImage to Upload in OMERO"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nTarget Dataset"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nOMERO server address"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nSelect Metadata Type"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Dataset\nMetadata File"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nROIs File"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["OMERO Image Import"];
  1 -->|output| 6;
  0 -->|output| 6;
  2 -->|output| 6;
  062f153f-4e64-47db-a940-eb552e6aae56["Output\nimage_upload_log"];
  6 --> 062f153f-4e64-47db-a940-eb552e6aae56;
  style 062f153f-4e64-47db-a940-eb552e6aae56 stroke:#2c3143,stroke-width:4px;
  7["Convert"];
  6 -->|log| 7;
  8["Replace Text"];
  7 -->|out_file1| 8;
  9["Split file"];
  8 -->|outfile| 9;
  10["Parse parameter value"];
  9 -->|list_output_tab| 10;
  11["OMERO Metadata Import"];
  4 -->|output| 11;
  3 -->|output| 11;
  10 -->|integer_param| 11;
  2 -->|output| 11;
  8fbe8e5a-9214-44f0-ab1f-5dc421963754["Output\nmetadata_import_log"];
  11 --> 8fbe8e5a-9214-44f0-ab1f-5dc421963754;
  style 8fbe8e5a-9214-44f0-ab1f-5dc421963754 stroke:#2c3143,stroke-width:4px;
  12["OMERO ROI Import"];
  10 -->|integer_param| 12;
  5 -->|output| 12;
  2 -->|output| 12;
  7b584a96-912c-4f74-9901-3d233b47f502["Output\nlog"];
  12 --> 7b584a96-912c-4f74-9901-3d233b47f502;
  style 7b584a96-912c-4f74-9901-3d233b47f502 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Image to Upload in OMERO
Input parameter Target Dataset
Input parameter OMERO server address
Input parameter Select Metadata Type
Input dataset Metadata File
Input dataset ROIs File

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy6 OMERO Image Import
toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy7 OMERO Metadata Import
toolshed.g2.bx.psu.edu/repos/ufz/omero_roi_import/omero_roi_import/5.18.0+galaxy5 OMERO ROI Import

Tools

Tool Links
Convert characters1
param_value_from_file
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy7 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ufz/omero_roi_import/omero_roi_import/5.18.0+galaxy5 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 5fc884fdd 2026-02-27 12:50:27 added .ga file for OMERO workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/omero-suite/workflows/2024_OMERO_Basic_Upload.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows