This guide explains you how to detect cells based on enhanced membranes using the pipeline with the Membrane Detection operation. The purpose of the pipeline is to identify cells starting from the membrane markers.
Detecting cells based on menbranes with enhancement
Introduction
Workflow
Activating the Sample Pipeline
- In the Shortcut Toolbar, click Analysis Panel
.
- In the Sample Pipelines list, double-click the Detect Cells based on Membranes with Enhancement Pipeline.
- If you have activated a pipeline, it will be replaced by the new one.
You can open the appropriate How to guide. By hovering over a pipeline, this button is displayed. When clicking on it, the option Open How to appears.
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.
Executing in a single run
As alternative to executing step by step, execute the pipeline in a single run.
- To run the whole pipeline, click
.
- To stop the pipeline execution, click
.
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.
Previewing the results
For all operations the preview is available in 2D, for some also in 3D.
- Switch from 2D Viewer
to 4D Viewer
in the Viewer Type Switch.
- To preview the operation results, click Preview
in the Operation toolbar.
Use the Navigator panel in the Panel Sidebar to select the preview z plane and/or time points.
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).
Adding or removing operations
You can add or remove operations from the sample pipeline.
- Click + Add operation...
- The operation list is grouped in four groups by their typology.
- To add the operation to the current pipeline, double-click it. Alternatively, drag & drop the operation to the current Pipeline.
Note: The operation cannot be added during the Pipeline execution. - The operation will be inserted at the end of the group of operations to which it belongs.
Voxel operations are positioned before the segment generation. Store operations are always put at the end of the Pipeline. - To remove an operation, click Close
at the Operation toolbar.