Detecting neurons

Introduction

This guide explains you how to detect neurons using the pipeline with the Neuron Tracer operation. The cell body is also detected, and it is used to start the tracing process. The operation offers algorithms to automatically segment neurons structures based on signal backbone seeds (local maxima) detection and their linking in a logical tree-like architecture. From the segments, several features are afterward measured.

Workflow

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.

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...
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.

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.