This guide explains you how to detect cells using the pipeline with the Cellpose-based Segmenter operation. The operation allows you to run a segmentation operation using a pretrained cellpose model on any dataset. You can use this operation in an analysis pipeline and in combination with all other analysis operations in the software.
Detecting cells (Cellpose-based Segmenter)
Introduction
Activating the Sample Pipeline
- In the Shortcut Toolbar, click Analysis Panel
.
- In the Sample Pipelines list, double-click the Detect cells Using Cellpose-based Segmenter 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.
Pipeline operations layout
The following operations are part of the pipeline.
Input ROI
This operation allows to select the region of interest (ROI). ROI defines the dataset subarea that will be processed and analyzed by the pipeline.
Input ROI parameters
|
Parameter |
Description |
|
|---|---|---|
|
ROI |
Sets the processing and analysis target space. |
|
|
– |
Current View |
The selected Z plane and the viewer area are processed. |
|
– |
Current Plane |
The selected Z plane is processed (XY). |
|
– |
Current Time Point |
The selected time point is processed (XYZ). |
|
– |
Current Image Set |
The complete dataset (XYZ and time) is processed. |
|
– |
Custom |
Allows to mix the previous methods. |
|
Channels |
Sets the processing and analysis target channels. Selecting a single channel, all the operations in the pipeline will be forced to use it. |
|
|
Scaling |
Sets the scaling of the dataset, which reduces it size. The measurements will not be modified by the scaling factor |
|
|
Crop input data |
Sets the limitation of the data used for the calculation to only the cropped selection defined above. If this option is not selected, the entire image set is used for the calculation. |
|
Additional Parameters
Additional settings for Input ROI expand, when you click in the operation.
|
Parameter |
Description |
|---|---|
|
Bounds |
Sets the analysis area edges. The whole XY bounds, the viewing area or a custom space can be applied. |
|
Planes |
Sets the analysis planes range. A single plane, a range of planes or the whole stack can be selected. |
|
Time Points |
Sets the analysis time points range. A single time pint, a range of time points or the whole movie can be selected. |
Cellpose-Based Segmenter
This operation detects automatically cells using pretrained cellpose models.
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 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
.
Viewing the results
- If not already visible, open the Objects dialog. In Shortcut Toolbar, click Objects table
.
- Measurements are now visible in the objects table.
- To add or remove table columns, click Feature Columns...
For more information, refer to the Online Help (F1).
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).