Workflow Type: Galaxy
Frozen
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Detecting a set of objects in an image, counting them and measuring certain characteristics about their morphology is probably the most frequently occurring task in bioimage analysis. Depending on the image, even this task could become quite challenging and the workflow could become quite complex. Here we start with a relatively simple image where combining a minimal set of image analysis components into a simple workflow does the job.
Steps
ID | Name | Description |
---|---|---|
0 | Threshold image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3 |
1 | Convert binary image to label map | toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0 |
2 | Colorize label map | toolshed.g2.bx.psu.edu/repos/imgteam/colorize_labels/colorize_labels/3.2.1+galaxy2 |
3 | Extract image features | toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
binary_image | #main/binary_image | n/a |
|
colorized_labelimage | #main/colorized_labelimage | n/a |
|
labelled_image | #main/labelled_image | n/a |
|
measurements | #main/measurements | n/a |
|
Version History
Version 1 (earliest) Created 17th Sep 2024 at 14:54 by yi.sun@embl.de
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Views: 577 Downloads: 114 Runs: 14
Created: 17th Sep 2024 at 14:54
Last updated: 18th Sep 2024 at 08:29
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