OMERO Nuclei Cell Counting, Image Import, Annotation and Region of Interests (ROIs) Workflow Version 1
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Run on GalaxyWorkflow to perform nuclei cell counting on High Content Screening (HCS) Data and upload result into OMERO
In this workflow, cell images are first uploaded to both Galaxy and OMERO using the “OMERO Image Import” tool. Concurrently, image processing is performed. After thresholding and binarization, key features of nuclei, such as area, label number, and perimeter, are computed from the processed images and saved as a CSV file. The result file is then attached to each image stored in OMERO using the “OMERO Metadata Import” tool. The “Label Extraction” tool generates ROI coordinates from the binary image, which are subsequently uploaded into OMERO using the “OMERO ROI Import” tool.
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 |
|
| OMERO server address | OMERO server address | Please enter a valid OMERO server address to upload your images to. |
|
| 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 |
|---|---|---|
| 3 | Convert image format | toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3 |
| 4 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
| 5 | Perform histogram equalization | toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0 |
| 6 | OMERO Image Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy3 |
| 7 | Convert | Convert characters1 |
| 8 | Filter 2-D image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1 |
| 9 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 10 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 11 | Threshold image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3 |
| 12 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 13 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 |
| 14 | Convert binary image to label map | toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0 |
| 15 | Analyze particles | toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary/20240614+galaxy0 |
| 16 | Parse parameter value | param_value_from_file |
| 17 | Parse parameter value | param_value_from_file |
| 18 | Extract image features | toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 |
| 19 | OMERO IDs | toolshed.g2.bx.psu.edu/repos/ufz/omero_filter/omero_filter/5.18.0+galaxy0 |
| 20 | Parse parameter value | param_value_from_file |
| 21 | OMERO Metadata Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy3 |
| 22 | 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 |
|
Version History
Version 1 (earliest) Created 28th Jan 2025 at 13:33 by Riccardo Massei
Initial commit
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Views: 35 Downloads: 7 Runs: 0
Created: 28th Jan 2025 at 13:33
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