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Detecting dendritic spines (Segments)

Introduction

The guide explains you how to trace dendritic spines using the Spine Tracer operation included in the Tracing module. The operation provides 3 methods (AI-assisted, Use Segments and Use Probability Map) to detect and connect dendritic spines to an already existing trace. This guide focuses on the segments method.

Workflow

Vertical flowchart: ROI selection → Neurite Tracer → Deep Learning Segmenter → Spine Tracer → 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 Spines with Use Segments Method pipeline.
    Analysis pane with '+ New Pipeline' button and Sample Pipelines list highlighting 'Detect Spines with Use Segments Method'
  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.

Viewing the results

  1. If not already visible, open the Objects dialog. In Shortcut Toolbar, click Objects table Objects window with Filter and Tags panel and a long list of Segment # entries with Volume, Volume (µm³) values 0,051–0,054 .
  2. Measurements are now visible in the objects table.
    Software Objects dialog with left filter showing Neuron Tracer tag and right table listing Trace #001, #002, and #003
  3. To color the results more meaningfully, click Set Object Style.
  4. Click Apply to: Traces.
     Style for tag: Neuron Tracer panel showing Apply to options with Traces selected and Color checked
  5. To select the trace color options, select one item from the Color by list.
    Traces options with Color by branch level selected and other color-by options listed
  6. To set further style settings, set the parameters in the Visualization section.
    Visualization panel with Opacity slider, Display choices Cone, Approximation, Skeleton and Material Standard and Glass

Refer to the Help (F1) for more Information.

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