ZEISS Microscopy Knowledge Base
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ZEISS Microscopy Knowledge Base

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.

  1. Switch from 2D Viewer 2D Viewer icon showing a monitor screen to 4D Viewer 4D Viewer icon showing a 3D cube in the Viewer Type Switch.
  2. To preview the operation results, click Preview Preview icon showing an eye symbol 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

  1. You have opened the pipeline.
  1. Go to the operation you want to change.
  2. Set the appropriate parameters as desired.
  3. Execute the pipeline (see Executing the pipeline).

Adding or removing operations

You can add or remove operations from the sample pipeline.

  1. Click + Add operation...
    Pipeline panel showing Input ROI: Current image set; Channels: All channels; Scaling 100% Include Z; + Add operation
  2. The operation list is grouped in four groups by their typology.
    Add Operation dialog with search box and list items 'Image processing', 'Segmentation', 'Use objects', 'Export'
  3. 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.
  4. 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.
  5. To remove an operation, click Close Small square gray icon showing an X symbol at the Operation toolbar.
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