2024_OMERO_Basic_Upload 1.0
Visit source
Download RO-Crate
Run on GalaxyBasic workflow to upload images into OMERO together with ROIs
Associated Tutorial
This workflows is part of the tutorial Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Riccardo Massei
Tutorial Author(s): Riccardo Massei
Tutorial Contributor(s): Björn Grüning, Riccardo Massei, Saskia Hiltemann, Martin Čech, Armin Dadras, Beatriz Serrano-Solano, Leonid Kostrykin
Funder(s): Deutsche Forschungsgemeinschaft, German Network for Bioinformatics Infrastructure Service, Training, Cooperations & Cloud Computing, University of Freiburg
Grants(s): NFDI4Bioimage
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Image to Upload in OMERO | Image to Upload in OMERO | Select the image file to upload into OMERO |
|
| Metadata File | Metadata File | Select the metadata file to upload into OMERO. Please refer to the tool "OMERO Metadata Import" to check how the file should be formatted |
|
| OMERO server address | OMERO server address | Please enter a valid OMERO server address to upload your images to. |
|
| ROIs File | ROIs File | Select the ROIs file to upload into OMERO. Please refer to the tool "OMERO ROIs Import" to check how the file should be formatted |
|
| Select Metadata Type | Select Metadata Type | Select if you want metadata as a table (please type "Table") or Key-Value Pairs (please type "Key-Value Pairs") |
|
| Target Dataset | Target Dataset | Select a target dataset to upload the image to. If the dataset name does not exist in OMERO, a new dataset will be created automatically. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | OMERO Image Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy6 |
| 7 | Convert | Convert characters1 |
| 8 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
| 9 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 |
| 10 | Parse parameter value | param_value_from_file |
| 11 | OMERO Metadata Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy7 |
| 12 | OMERO ROI Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_roi_import/omero_roi_import/5.18.0+galaxy5 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| image_upload_log | image_upload_log | n/a |
|
| metadata_import_log | metadata_import_log | n/a |
|
| log | log | n/a |
|
Version History
master
Creators and Submitter
Views: 310 Downloads: 56 Runs: 0
Created: 9th Mar 2026 at 13:26
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
