ZEISS Knowledge Base

Activating the Sample Pipeline

In the Shortcut Toolbar, click Analysis Panel .
In the Sample Pipelines list, double-click the Detect Neurites 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.

The following operations are part of the pipeline.

This operation allows to select the region of interest (ROI). ROI defines the dataset subarea that will be processed and analyzed by the pipeline.

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. Note: Use the Custom option during the pipeline setting and testing. Set a sub volume (XY, Planes, Time Points, channels) of your dataset on which perform the trial. This will speed up the setting process.
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.

Neurite Tracer

Automatic tubular-like structures detection based on the threshold-based reconstruction algorithm.

Store Objects

Store the detected segments (tag) in the active dataset.

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 .

Operation status

Executing buttons in the Operation toolbar after executing

When the operation is running, this icon is shown.

When the operation is completed, this icon is shown.

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 color the results more meaningfully, click Set Object Style.
Click Apply to: Traces.
To select the trace color options, select one item from the Color by list.

For some visualization examples, see Visualization examples.
To set further style settings, set the parameters in the Visualization section.

For some visualization examples, see Visualization examples.

Refer to the Help (F1) for more Information.

Visualization examples

Color by structure - Cone

Color by structure - Approximation

Color by depth - Approximation

Color by depth - Skeleton

Color by depth - Cone

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).

Editing the traces

The tubular structures segmented (traces) by the operation can be edited. Branches, terminal points, branches points, and other trace components are accessible for modification, optimizations, and improvements.

In the Shortcut toolbar, click Trace Tool .
An Option Bar below the Shortcut Toolbar is displayed. Here you can find various tools with which you can draw or edit traces.
Most of these tools can be activated using simple shortcuts to facilitate the workflow.

Refer to the Help (F1) for more details.

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Detecting neurites

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