This guide explains you how to detect small structures using watershed using the pipeline with the Normalization and Watershed operation. The purpose of the pipeline is to detect objects having almost any shape. The pipeline can be applied to cells, nuclei, or any kind of small particles.
Detecting small structures (Watershed)
Introduction
Workflow
Executing the pipeline
You can execute the pipeline step by step or in a single run. To do this, use the executing buttons in the Pipeline toolbar.
Executing step by step
You can execute the pipeline step by step (back and forth). This method allows to run and undo a single operation. You can either use the executing buttons in the Pipeline toolbar or in the Operation toolbar to go through the operation list.
- To run the single operation, click
.
- To undo the single operation, click
.
Note: Undo the last operation executed if you need to change the operation settings.
Operation status
When the operation is running, this icon is shown.
When the operation is completed, this icon is shown.
Modifying the current pipeline
You can modify the pipeline to adapt to another datasets. Therefore, all the pipeline parameters should be set according to the new dataset features.
Adjusting the operations
The parameters of each operation are described here: Pipeline operations layout
- You have opened the pipeline.
- Go to the operation you want to change.
- Set the appropriate parameters as desired.
- Execute the pipeline (see Executing the pipeline).