OMERO Image Import, Annotation and Region of Interests (ROIs) Workflow Version 1
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Run on GalaxyGeneral workflow to upload data into OMERO using Galaxy
A dataset for testing can be found at: https://zenodo.org/records/14205500
Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.
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+galaxy3 |
| 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+galaxy3 |
| 12 | OMERO ROI Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_roi_import/omero_roi_import/5.18.0+galaxy4 |
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
Version 1 (earliest) Created 28th Jan 2025 at 13:17 by Riccardo Massei
Initial commit
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Views: 37 Downloads: 4 Runs: 0
Created: 28th Jan 2025 at 13:17
AttributionsNone
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https://orcid.org/0000-0003-2104-9519
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