Voronoi segmentation 1.0
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Run on GalaxyGeneric workflow to perform Voronoi segmentation. Input requirements:
- Image: -- Preferably lighter objects on a darker background for the mask to work well. -- Format: .tiff, stored in planar RGB format, not interleaved (http://avitevet.com/uncategorized/when-to-use-it-interleaved-vs-planar-image-data-storage/).
- Seeds: -- White seeds on a black background -- Format: .tiff
Associated Tutorial
This workflows is part of the tutorial Voronoi segmentation, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Even Moa Myklebust, Riccardo Massei
Tutorial Author(s): Even Moa Myklebust, Riccardo Massei, Leonid Kostrykin, Anne Fouilloux
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Image | #main/Image | Image to be segmented. |
|
| Seeds | #main/Seeds | Seeds for the Voronoi segmentation. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Convert image format | toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3 |
| 3 | Convert binary image to label map | toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0 |
| 4 | Convert single-channel to multi-channel image | toolshed.g2.bx.psu.edu/repos/imgteam/repeat_channels/repeat_channels/1.26.4+galaxy0 |
| 5 | Filter 2-D image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1 |
| 6 | Compute Voronoi tessellation | toolshed.g2.bx.psu.edu/repos/imgteam/voronoi_tesselation/voronoi_tessellation/0.22.0+galaxy3 |
| 7 | Threshold image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3 |
| 8 | Count objects in label map | toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2 |
| 9 | Extract image features | toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 |
| 10 | Process images using arithmetic expressions | toolshed.g2.bx.psu.edu/repos/imgteam/image_math/image_math/1.26.4+galaxy2 |
| 11 | Colorize label map | toolshed.g2.bx.psu.edu/repos/imgteam/colorize_labels/colorize_labels/3.2.1+galaxy3 |
| 12 | Overlay images | toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Single channel image | #main/Single channel image | n/a |
|
| Smoothed image | #main/Smoothed image | n/a |
|
| colorized label map | #main/colorized label map | n/a |
|
| image features | #main/image features | n/a |
|
| label map | #main/label map | n/a |
|
| mask | #main/mask | n/a |
|
| multi-channel image | #main/multi-channel image | n/a |
|
| object count | #main/object count | n/a |
|
| segmentation | #main/segmentation | n/a |
|
| segmented image | #main/segmented image | n/a |
|
| tesselation | #main/tesselation | n/a |
|
Version History
master
Creators and Submitter
Views: 33 Downloads: 2 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
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Organizations: Galaxy
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