Workflow Type: Galaxy
Frozen
This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html
Inputs
ID | Name | Description | Type |
---|---|---|---|
input_image | #main/input_image | The fluorescence microscopy images to be segmented. Must be the single image channel, which contains the cell nuclei. |
|
Steps
ID | Name | Description |
---|---|---|
1 | Filter 2D image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3 |
2 | Perform histogram equalization | toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1-2 |
3 | Threshold image | toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2 |
4 | Convert image format | toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy2 |
5 | Convert binary image to label map | toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0 |
6 | Overlay images | toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy0 |
7 | Count objects in label map | toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
label_image | #main/label_image | n/a |
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objects_count | #main/objects_count | n/a |
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overlay_image | #main/overlay_image | n/a |
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Version History
v0.1 (earliest) Created 1st Mar 2024 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
f66ee02
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Views: 1799 Downloads: 206 Runs: 1
Created: 1st Mar 2024 at 03:01
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