ZEISS Knowledge Base

The pipeline has to be created according to the user analysis requirements as well as the sample typology.

The sample labeling, the imaging technique (Fluorescence, EM, Tomography, bright-field ...) and the image characteristics are important to drive the pipeline setup.

The knowledge of the biological structures under evaluation, it’s behavior and the expected features' trend are also important as well. All the above information should be used to build a target driven pipeline.

To achieve the application note goals, only a couple of operators are mandatory, as described below:

Change the ROI operator parameters inside the Input ROI dialog.
A dropdown menu will open.
Inside the dropdown menu, set the processing and analysis target space.

Following options are available:
Current View: The selected Z plane and the viewer area will be processed.
Current Plane: The selected Z plane will be processed (XY).
Current Image Set: The complete dataset (XYZ and time) will be processed.
Current Time Point: The selected time point will be processed (XYZ).
Custom: Allows to mix the previous methods and expands the Input ROI dialog.
NOTE: Use the Custom option during setting and testing of the pipeline. Set a sub volume (XY, Planes, Time Points, channels) of your dataset on which to perform the trial. This will speed up the setting process.
Use the Custom option during setting and testing of the pipeline. Setting a sub volume of your dataset on which to perform the trial, will speed up the setting process. You have the following setting options:
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 TP, a range of TPs or the whole movie can be selected.

Channels: Sets the processing and analysis target channels. Selecting a single channel, all the operators in the pipeline will be forced to use it.

Scaling: Scales the dataset by reducing the size. The measurements will not be modified by the scaling factor.
Set the Import Document Objects operator, by selecting the Tag filter inside the Import Document Objects dialog .
The select tags dialog opens.
Select the Manual TAG and use the right arrow button to move the TAG to the right table.
Add or remove optional operators inside the pipeline.
The Analysis Pipeline panel consists of two main areas. The Pipeline area and the Analysis Operations area.
Add the Operators to the pipeline in two possible ways:
1. Double-click on the Operator you wish to add to the current pipeline. The Operator will be inserted at the end of the group of operations to which it belongs. Voxel operations are positioned before the Segment generation meanwhile Store operations are put always at the end of the pipeline.
2. Drag and drop the Operator you wish to add to the current pipeline. The Operator will be automatically inserted in any place within the group of operations to which it belongs. NOTE: The Operator cannot be added during the pipeline execution.
To remove an Operator from the pipeline, press the X button located in the right side of the operator title bar.