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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

Flowchart: ROI selection arrow to Cell Body segmentation arrow to Neuron Tracer dashed arrow to Export data (optional)

Activating the Sample Pipeline

  1. In the Shortcut Toolbar, click Analysis Panel Toolbar showing menus File Edit View Data Navigation Objects Analysis Extras Window Help and tool icons.
    Analysis panel showing Document Pipelines and Sample Pipelines list with Compartmentalize Cells or Particles highlighted
  2. In the Sample Pipelines list, double-click the Detect Neurons Pipeline.
    Analysis panel showing Document Pipelines and Sample Pipelines list with Detect Neurons highlighted
  3. 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 Hamburger menu icon showing three horizontal lines is displayed. When clicking on it, the option Open How to appears.

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.

  1. In the Shortcut toolbar, click Trace Tool White branched neurite traces on black background with yellow terminals, magenta branch point and 'Color by Structure' legend.
    White branched neurite traces on black background with yellow neurite segments, orange fragments and a magenta branch point.
  2. An Option Bar below the Shortcut Toolbar is displayed. Here you can find various tools with which you can draw or edit traces.
    Y-shaped white traces with yellow neurite markers, a magenta branch-point marker and orange primary path fragments on black
    Gray Y-shaped trace with yellow Neurite markers, magenta Branch Point, orange Primary Path, legend Color by Structure
  3. 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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